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refactoring

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frankknoll
2022-02-07 21:11:37 +01:00
parent c0a7c85bf0
commit 4900629f42
1 changed files with 26 additions and 30 deletions
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54
HowBadIsMyBatch.ipynb
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@@ -208,19 +208,30 @@
"source": [ "source": [
"import pandas as pd\n", "import pandas as pd\n",
"\n", "\n",
"class BatchCodeTableHelper:\n", "class BatchCodeTableFactory:\n",
"\n", "\n",
" def __init__(self, dataFrame : pd.DataFrame):\n", " @staticmethod\n",
" self.dataFrame = dataFrame\n", " def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, manufacturer = manufacturer, dose = dose)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES']]\n",
"\n", "\n",
" # create table from https://www.howbadismybatch.com/combined.html\n", " # create table from https://www.howbadismybatch.com/combined.html\n",
" def createSevereEffectsBatchCodeTable(self):\n", " @staticmethod\n",
" batchCodeTable = SummationTableFactory.createSummationTable(self.dataFrame.groupby('VAX_LOT'))\n", " def createSevereEffectsBatchCodeTable(dataFrame : pd.DataFrame, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, dose = dose)\n",
" return BatchCodeTableFactory._createSummationTableByVAX_LOT(dataFrame)\n",
"\n",
" @staticmethod\n",
" def _createSummationTableByVAX_LOT(dataFrame):\n",
" batchCodeTable = SummationTableFactory.createSummationTable(dataFrame.groupby('VAX_LOT'))\n",
" batchCodeTable = batchCodeTable[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES', 'HOSPITALISATIONS', 'EMERGENCY ROOM OR DOCTOR VISITS']]\n", " batchCodeTable = batchCodeTable[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES', 'HOSPITALISATIONS', 'EMERGENCY ROOM OR DOCTOR VISITS']]\n",
" batchCodeTable = batchCodeTable.sort_values(by = 'ADRs', ascending = False)\n", " batchCodeTable = batchCodeTable.sort_values(by = 'ADRs', ascending = False)\n",
" return self._addCompanyColumn(batchCodeTable, self._createCompanyByBatchCodeTable())\n", " return BatchCodeTableFactory._addCompanyColumn(batchCodeTable, BatchCodeTableFactory._createCompanyByBatchCodeTable(dataFrame))\n",
"\n", "\n",
" def _addCompanyColumn(self, batchCodeTable, companyByBatchCodeTable):\n", " @staticmethod\n",
" def _addCompanyColumn(batchCodeTable, companyByBatchCodeTable):\n",
" return pd.merge(\n", " return pd.merge(\n",
" batchCodeTable,\n", " batchCodeTable,\n",
" companyByBatchCodeTable,\n", " companyByBatchCodeTable,\n",
@@ -229,29 +240,15 @@
" right_index = True,\n", " right_index = True,\n",
" validate = 'one_to_one')\n", " validate = 'one_to_one')\n",
"\n", "\n",
" def _createCompanyByBatchCodeTable(self):\n", " @staticmethod\n",
" return self._createManufacturerByBatchCodeTable().rename(columns = {\"VAX_MANU\": \"COMPANY\"})\n", " def _createCompanyByBatchCodeTable(dataFrame):\n",
" return BatchCodeTableFactory._createManufacturerByBatchCodeTable(dataFrame).rename(columns = {\"VAX_MANU\": \"COMPANY\"})\n",
"\n", "\n",
" def _createManufacturerByBatchCodeTable(self):\n", " @staticmethod\n",
" manufacturerByBatchCodeTable = self.dataFrame[['VAX_LOT', 'VAX_MANU']]\n", " def _createManufacturerByBatchCodeTable(dataFrame):\n",
" manufacturerByBatchCodeTable = dataFrame[['VAX_LOT', 'VAX_MANU']]\n",
" manufacturerByBatchCodeTable = manufacturerByBatchCodeTable.drop_duplicates(subset = ['VAX_LOT'])\n", " manufacturerByBatchCodeTable = manufacturerByBatchCodeTable.drop_duplicates(subset = ['VAX_LOT'])\n",
" return manufacturerByBatchCodeTable.set_index('VAX_LOT')\n", " return manufacturerByBatchCodeTable.set_index('VAX_LOT')\n"
"\n",
"\n",
"class BatchCodeTableFactory:\n",
"\n",
" @staticmethod\n",
" def createBatchCodeTable(dataFrame : pd.DataFrame, manufacturer, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, manufacturer = manufacturer, dose = dose)\n",
" return BatchCodeTableHelper(dataFrame).createSevereEffectsBatchCodeTable()[['ADRs', 'DEATHS', 'DISABILITIES', 'LIFE THREATENING ILLNESSES']]\n",
"\n",
" # create table from https://www.howbadismybatch.com/combined.html\n",
" @staticmethod\n",
" def createSevereEffectsBatchCodeTable(dataFrame : pd.DataFrame, dose):\n",
" dataFrame = DataFrameFilter().filterByCovid19(dataFrame)\n",
" dataFrame = DataFrameFilter().filterBy(dataFrame, dose = dose)\n",
" return BatchCodeTableHelper(dataFrame).createSevereEffectsBatchCodeTable()\n"
] ]
}, },
{ {
@@ -281,7 +278,6 @@
" dataFrame['VAX_DOSE_SERIES'].rename('Dose')\n", " dataFrame['VAX_DOSE_SERIES'].rename('Dose')\n",
" ]))\n", " ]))\n",
"\n", "\n",
" # FK-TODO: DRY because it generates a subset of BatchCodeTableHelper.createSevereEffectsBatchCodeTable()\n",
" @staticmethod\n", " @staticmethod\n",
" def _getDoseTable(dataFrame):\n", " def _getDoseTable(dataFrame):\n",
" doseTable = SummationTableFactory.createSummationTable(\n", " doseTable = SummationTableFactory.createSummationTable(\n",