refactoring
This commit is contained in:
frankknoll
@@ -224,23 +224,52 @@
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"class DoseAnalysis:\n",
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" \n",
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" @staticmethod\n",
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" def getNthDoseTable(dataFrame, dose):\n",
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" return pd.DataFrame(DoseAnalysis._getNthDoseDict(DataFrameFilter(dataFrame).filterBy(dose = dose)))\n",
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" def getDoseTable(dataFrame):\n",
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" # FK-TODO: _convertColumnsOfDataFrameToNumerics() sollte schon während des Einlesens aus den CSV-Dateien durchgeführt werden\n",
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" # FK-TODO: bitte alle DataFrames als unmutable behandeln und nicht inplace ändern.\n",
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" DoseAnalysis._convertColumnsOfDataFrameToNumerics(dataFrame, ['DIED', 'L_THREAT', 'DISABLE'])\n",
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" return pd.DataFrame(DoseAnalysis._getNthDoseDict(dataFrame))\n",
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"\n",
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" # FK-TODO: inline method\n",
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" @staticmethod\n",
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" def _getNthDoseDict(df):\n",
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" nthDoseDict = {\n",
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" 'Total reports': [len(df.index)],\n",
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" 'Deaths': [DoseAnalysis._count(df, 'DIED')],\n",
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" 'Disabilities': [DoseAnalysis._count(df, 'DISABLE')],\n",
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" 'Life Threatening Illnesses': [DoseAnalysis._count(df, 'L_THREAT')]\n",
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" }\n",
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" nthDoseDict['Severe reports (%)'] = [(nthDoseDict['Deaths'][0] + nthDoseDict['Disabilities'][0] + nthDoseDict['Life Threatening Illnesses'][0]) / nthDoseDict['Total reports'][0] * 100]\n",
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" return nthDoseDict\n",
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" doseTable = df.groupby('VAX_DOSE_SERIES').agg(\n",
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" {\n",
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" 'DIED': ['sum', 'size'],\n",
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" 'L_THREAT': 'sum',\n",
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" 'DISABLE': 'sum'\n",
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" })\n",
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" DoseAnalysis._flattenColumns(doseTable)\n",
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" doseTable = doseTable.rename(\n",
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" columns =\n",
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" {\n",
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" \"DIED_size\": \"Total reports\",\n",
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" \"DIED_sum\": \"Deaths\",\n",
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" \"L_THREAT_sum\": \"Life Threatening Illnesses\",\n",
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" \"DISABLE_sum\": \"Disabilities\"\n",
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" })[['Total reports', 'Deaths', 'Disabilities', 'Life Threatening Illnesses']]\n",
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" doseTable['Severe reports (%)'] = (doseTable['Deaths'] + doseTable['Disabilities'] + doseTable['Life Threatening Illnesses']) / doseTable['Total reports'] * 100\n",
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" return doseTable\n",
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"\n",
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" @staticmethod\n",
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" def _count(dataFrame, column):\n",
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" return len(dataFrame[dataFrame[column] == 'Y'])\n"
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" return len(dataFrame[dataFrame[column] == 'Y'])\n",
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"\n",
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" # FK-TODO: DRY with BatchCodeTableHelper\n",
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" @staticmethod\n",
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" def _convertColumnsOfDataFrameToNumerics(dataFrame, columns):\n",
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" for column in columns:\n",
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" DoseAnalysis._convertColumnOfDataFrameToNumeric(dataFrame, column)\n",
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"\n",
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" # FK-TODO: DRY with BatchCodeTableHelper\n",
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" @staticmethod\n",
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" def _convertColumnOfDataFrameToNumeric(dataFrame, column):\n",
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" dataFrame[column] = np.where(dataFrame[column] == 'Y', 1, 0)\n",
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"\n",
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" # FK-TODO: DRY with BatchCodeTableHelper\n",
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" @staticmethod\n",
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" def _flattenColumns(batchCodeTable):\n",
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" batchCodeTable.columns = [\"_\".join(a) for a in batchCodeTable.columns.to_flat_index()]\n"
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]
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},
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{
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@@ -557,57 +586,35 @@
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"\n",
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"class DoseAnalysisTest(unittest.TestCase):\n",
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"\n",
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" def test_getFirstDoseTable(self):\n",
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" self._test_getNthDoseTable(\n",
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" dataFrame = self.createDataFrame(\n",
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" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
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" data = [ ['Y', np.NaN, np.NaN,\t 'COVID19', 'MODERNA', '016M20A', '2'],\n",
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" ['Y', np.NaN, np.NaN, 'COVID19', 'MODERNA', '030L20A', '1'],\n",
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" ['Y', 'Y', 'Y', 'COVID19', 'MODERNA', '030L20B', '1']],\n",
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" index = [\n",
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" \"1048786\",\n",
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" \"1048786\",\n",
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" \"4711\"],\n",
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" dtypes = {'VAX_DOSE_SERIES': \"string\"}),\n",
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" dose = '1',\n",
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" doseTableExpected = pd.DataFrame(\n",
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" {\n",
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" 'Total reports': [2],\n",
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" 'Deaths': [2],\n",
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" 'Disabilities': [1],\n",
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" 'Life Threatening Illnesses': [1],\n",
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" 'Severe reports (%)': [(2 + 1 + 1)/2 * 100]\n",
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" }))\n",
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"\n",
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" def test_getSecondDoseTable(self):\n",
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" self._test_getNthDoseTable(\n",
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" dataFrame = self.createDataFrame(\n",
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" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
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" data = [ ['Y', np.NaN, np.NaN,\t 'COVID19', 'MODERNA', '016M20A', '2'],\n",
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" ['Y', np.NaN, np.NaN, 'COVID19', 'MODERNA', '030L20A', '1'],\n",
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" ['Y', 'Y', 'Y', 'COVID19', 'MODERNA', '030L20B', '1']],\n",
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" index = [\n",
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" \"1048786\",\n",
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" \"1048786\",\n",
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" \"4711\"],\n",
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" dtypes = {'VAX_DOSE_SERIES': \"string\"}),\n",
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" dose = '2',\n",
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" doseTableExpected = pd.DataFrame(\n",
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" {\n",
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" 'Total reports': [1],\n",
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" 'Deaths': [1],\n",
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" 'Disabilities': [0],\n",
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" 'Life Threatening Illnesses': [0],\n",
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" 'Severe reports (%)': [(1 + 0 + 0)/1 * 100]\n",
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" }))\n",
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"\n",
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" def _test_getNthDoseTable(self, dataFrame, dose, doseTableExpected):\n",
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" # When\n",
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" doseTable = DoseAnalysis.getNthDoseTable(dataFrame, dose)\n",
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" def test_getDoseTable(self):\n",
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" # Given\n",
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" dataFrame = self.createDataFrame(\n",
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" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
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" data = [ ['Y', np.NaN, np.NaN,\t 'COVID19', 'MODERNA', '016M20A', '2'],\n",
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" ['Y', np.NaN, np.NaN, 'COVID19', 'MODERNA', '030L20A', '1'],\n",
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" ['Y', 'Y', 'Y', 'COVID19', 'MODERNA', '030L20B', '1']],\n",
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" index = [\n",
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" \"1048786\",\n",
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" \"1048786\",\n",
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" \"4711\"],\n",
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" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
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" \n",
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" # Then\n",
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" assert_frame_equal(doseTable, doseTableExpected)\n",
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" # When\n",
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" doseTable = DoseAnalysis.getDoseTable(dataFrame)\n",
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"\n",
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" # Then\n",
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" assert_frame_equal(\n",
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" doseTable,\n",
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" pd.DataFrame(\n",
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" data = {\n",
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" 'Total reports': [2, 1],\n",
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" 'Deaths': [2, 1],\n",
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" 'Disabilities': [1, 0],\n",
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" 'Life Threatening Illnesses': [1, 0],\n",
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" 'Severe reports (%)': [(2 + 1 + 1)/2 * 100, (1 + 0 + 0)/1 * 100]\n",
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" },\n",
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" index = pd.Index(['1', '2'], dtype = \"string\", name = 'VAX_DOSE_SERIES')))\n",
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" \n",
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" def createDataFrame(self, index, columns, data, dtypes = {}):\n",
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" return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
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]
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@@ -691,10 +698,10 @@
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"source": [
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"# https://www.howbadismybatch.com/firstsecond.html\n",
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"\n",
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"def getNthDoseTable(dose):\n",
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"def getDoseTable():\n",
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" vaersDescrs = VaersDescrReader(dataDir = \"VAERS\").readAllVaersDescrs()\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" return DoseAnalysis.getNthDoseTable(dataFrame, dose)"
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" return DoseAnalysis.getDoseTable(dataFrame)"
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]
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},
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{
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@@ -704,17 +711,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"getNthDoseTable(dose = '1')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "686d4ddf",
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"metadata": {},
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"outputs": [],
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"source": [
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"getNthDoseTable(dose = '2')"
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"getDoseTable()"
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]
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}
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],
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