refactoring
This commit is contained in:
frankknoll
@@ -2,7 +2,7 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": null,
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"id": "9de5907f-18f5-4cb1-903e-26028ff1fa03",
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"metadata": {},
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"outputs": [],
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@@ -16,7 +16,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": null,
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"id": "a271254b",
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"metadata": {},
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"outputs": [],
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@@ -60,7 +60,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": null,
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"id": "7b5d6df0",
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"metadata": {},
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"outputs": [],
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@@ -87,7 +87,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"id": "3ebcba86",
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"metadata": {},
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"outputs": [],
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@@ -96,21 +96,23 @@
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"\n",
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"class DataFrameFilter:\n",
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" \n",
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" @staticmethod\n",
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" def filterDataFrame(df, manufacturer = None, dose = None):\n",
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" isCovid19 = df[\"VAX_TYPE\"] == \"COVID19\"\n",
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" isManufacturer = df[\"VAX_MANU\"] == manufacturer if manufacturer is not None else True\n",
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" isDose = df[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n",
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" return df[isCovid19 & isManufacturer & isDose]\n",
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" def __init__(self, dataFrame):\n",
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" self.dataFrame = dataFrame \n",
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"\n",
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" @staticmethod\n",
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" def filterDataFrameForSevereEffects(df, dose):\n",
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" return DataFrameFilter.filterDataFrame(df, dose = dose)\n"
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" def filterBy(self, manufacturer = None, dose = None):\n",
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" # FK-TODO: extract private instance methods\n",
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" isCovid19 = self.dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n",
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" isManufacturer = self.dataFrame[\"VAX_MANU\"] == manufacturer if manufacturer is not None else True\n",
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" isDose = self.dataFrame[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n",
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" return self.dataFrame[isCovid19 & isManufacturer & isDose]\n",
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"\n",
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" def filterForSevereEffects(self, dose):\n",
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" return self.filterBy(dose = dose)\n"
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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": 5,
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"execution_count": null,
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"id": "99945ca8",
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"metadata": {},
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"outputs": [],
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@@ -164,7 +166,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": null,
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"id": "3dacedfd",
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"metadata": {},
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"outputs": [],
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@@ -174,7 +176,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 7,
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"execution_count": null,
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"id": "e59a1825",
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"metadata": {},
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"outputs": [],
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@@ -224,7 +226,7 @@
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" \n",
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" # When\n",
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" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
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" dataFrame = DataFrameFilter(dataFrame).filterBy(manufacturer = \"MODERNA\", dose = '1')\n",
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" \n",
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" # Then\n",
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" dataFrameExpected = self.createDataFrame(\n",
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@@ -263,7 +265,7 @@
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" \n",
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" # When\n",
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" dataFrame = DataFrameFilter.filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
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" dataFrame = DataFrameFilter(dataFrame).filterForSevereEffects(dose = '1')\n",
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" \n",
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" # Then\n",
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" dataFrameExpected = self.createDataFrame(\n",
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@@ -298,7 +300,7 @@
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" \n",
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" # When\n",
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" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
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" dataFrame = DataFrameFilter(dataFrame).filterBy(manufacturer = \"MODERNA\", dose = '1')\n",
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" \n",
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" # Then\n",
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" dataFrameExpected = self.createDataFrame(\n",
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@@ -331,7 +333,7 @@
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" \n",
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" # When\n",
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" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
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" dataFrame = DataFrameFilter(dataFrame).filterBy(manufacturer = \"MODERNA\", dose = '2')\n",
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" \n",
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" # Then\n",
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" dataFrameExpected = self.createDataFrame(\n",
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@@ -348,7 +350,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": null,
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"id": "e14465d7",
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"metadata": {},
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"outputs": [],
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@@ -395,14 +397,14 @@
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" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
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" }\n",
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" ])\n",
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" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
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" dataFrame = DataFrameFilter(dataFrame).filterBy(manufacturer = \"MODERNA\", dose = '1')\n",
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" self._test_createBatchCodeTable(dataFrame);\n",
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"\n",
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" def test_createBatchCodeTable(self):\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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" VaersDescrReader(\"test/VAERS\").readAllVaersDescrs())\n",
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" self._test_createBatchCodeTable(\n",
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" DataFrameFilter.filterDataFrame(\n",
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" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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" VaersDescrReader(\"test/VAERS\").readAllVaersDescrs()),\n",
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" DataFrameFilter(dataFrame).filterBy(\n",
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" manufacturer = \"MODERNA\",\n",
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" dose = '1'))\n",
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"\n",
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@@ -427,7 +429,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": null,
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"id": "ded70c87",
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"metadata": {},
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"outputs": [],
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@@ -459,7 +461,7 @@
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" }\n",
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" ]\n",
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" )\n",
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" dataFrame = DataFrameFilter.filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
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" dataFrame = DataFrameFilter(dataFrame).filterForSevereEffects(dose = '1')\n",
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"\n",
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" # When\n",
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" batchCodeTable = createSevereEffectsBatchCodeTable(dataFrame)\n",
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@@ -484,509 +486,36 @@
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"execution_count": null,
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"id": "5a8bff1b",
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"test_createBatchCodeTable (__main__.BatchCodeTableTest) ... ok\n",
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"test_createBatchCodeTable2 (__main__.BatchCodeTableTest) ... ok\n",
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"test_createAndFilterDataFrameFromDescrs (__main__.CreateAndFilterDataFrameTest) ... ok\n",
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"test_createAndFilterDataFrameFromDescrsWithFirstDose (__main__.CreateAndFilterDataFrameTest) ... ok\n",
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"test_createAndFilterDataFrameFromDescrsWithSecondDose (__main__.CreateAndFilterDataFrameTest) ... ok\n",
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"test_createDataFrameFromForSevereEffects (__main__.CreateAndFilterDataFrameTest) ... ok\n",
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"test_createSevereEffectsBatchCodeTable (__main__.SevereEffectsBatchCodeTableTest) ... ok\n",
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"\n",
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"----------------------------------------------------------------------\n",
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"Ran 7 tests in 0.156s\n",
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"\n",
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"OK\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"<unittest.main.TestProgram at 0x7f8aa7824220>"
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]
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},
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"execution_count": 10,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"outputs": [],
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"source": [
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"unittest.main(argv = [''], verbosity = 2, exit = False)"
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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": 11,
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"execution_count": null,
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"id": "86e0e4f2",
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"metadata": {},
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"outputs": [],
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"source": [
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"def saveBatchCodeTable(manufacturer, excelFile):\n",
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" batchCodeTable = createBatchCodeTable(\n",
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" DataFrameFilter.filterDataFrame(\n",
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" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
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" manufacturer = manufacturer,\n",
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" dose = '1'))\n",
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" vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" dataFrameFilter = DataFrameFilter(dataFrame)\n",
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" batchCodeTable = createBatchCodeTable(dataFrameFilter.filterBy(manufacturer = manufacturer, dose = '1'))\n",
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" display(manufacturer, batchCodeTable)\n",
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" batchCodeTable.to_excel(excelFile)"
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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": 12,
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"execution_count": null,
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"id": "ab170c16",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'MODERNA'"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead th {\n",
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" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>ADRs</th>\n",
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" <th>DEATHS</th>\n",
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" <th>DISABILITIES</th>\n",
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" <th>LIFE THREATENING ILLNESSES</th>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>VAX_LOT</th>\n",
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" <th></th>\n",
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" <th></th>\n",
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" <th></th>\n",
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" <th></th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>039K20A</th>\n",
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" <td>3330</td>\n",
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" <td>67.0</td>\n",
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" <td>22.0</td>\n",
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" <td>29.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>026L20A</th>\n",
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" <td>3327</td>\n",
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" <td>25.0</td>\n",
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" <td>24.0</td>\n",
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" <td>21.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>011J20A</th>\n",
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" <td>3072</td>\n",
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" <td>33.0</td>\n",
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" <td>27.0</td>\n",
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" <td>26.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>025L20A</th>\n",
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" <td>2391</td>\n",
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" <td>42.0</td>\n",
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" <td>16.0</td>\n",
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" <td>26.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>012L20A</th>\n",
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" <td>2352</td>\n",
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" <td>57.0</td>\n",
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" <td>28.0</td>\n",
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" <td>22.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>...</th>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" <td>...</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>028-20A</th>\n",
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" <td>1</td>\n",
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" <td>0.0</td>\n",
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||||
" <td>0.0</td>\n",
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||||
" <td>0.0</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>028(L or Z?)20A</th>\n",
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" <td>1</td>\n",
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||||
" <td>0.0</td>\n",
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||||
" <td>0.0</td>\n",
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||||
" <td>0.0</td>\n",
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||||
" </tr>\n",
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" <tr>\n",
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" <th>028 L20A</th>\n",
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||||
" <td>1</td>\n",
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||||
" <td>0.0</td>\n",
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||||
" <td>0.0</td>\n",
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||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
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" <tr>\n",
|
||||
" <th>028 L 20A</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>xx3A21A</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" </tbody>\n",
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||||
"</table>\n",
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"<p>10248 rows × 4 columns</p>\n",
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"</div>"
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],
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"text/plain": [
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" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
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"VAX_LOT \n",
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"039K20A 3330 67.0 22.0 29.0\n",
|
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"026L20A 3327 25.0 24.0 21.0\n",
|
||||
"011J20A 3072 33.0 27.0 26.0\n",
|
||||
"025L20A 2391 42.0 16.0 26.0\n",
|
||||
"012L20A 2352 57.0 28.0 22.0\n",
|
||||
"... ... ... ... ...\n",
|
||||
"028-20A 1 0.0 0.0 0.0\n",
|
||||
"028(L or Z?)20A 1 0.0 0.0 0.0\n",
|
||||
"028 L20A 1 0.0 0.0 0.0\n",
|
||||
"028 L 20A 1 0.0 0.0 0.0\n",
|
||||
"xx3A21A 1 0.0 0.0 0.0\n",
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"\n",
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"[10248 rows x 4 columns]"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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||||
"text/plain": [
|
||||
"'PFIZER\\\\BIONTECH'"
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||||
]
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||||
},
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||||
"metadata": {},
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"output_type": "display_data"
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},
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{
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"data": {
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||||
"text/html": [
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||||
"<div>\n",
|
||||
"<style scoped>\n",
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||||
" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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||||
" }\n",
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||||
"\n",
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||||
" .dataframe tbody tr th {\n",
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||||
" vertical-align: top;\n",
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||||
" }\n",
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||||
"\n",
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||||
" .dataframe thead th {\n",
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||||
" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
|
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" <th>ADRs</th>\n",
|
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" <th>DEATHS</th>\n",
|
||||
" <th>DISABILITIES</th>\n",
|
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" <th>LIFE THREATENING ILLNESSES</th>\n",
|
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" </tr>\n",
|
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" <tr>\n",
|
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" <th>VAX_LOT</th>\n",
|
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" <th></th>\n",
|
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" <th></th>\n",
|
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" <th></th>\n",
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" <th></th>\n",
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" </tr>\n",
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" </thead>\n",
|
||||
" <tbody>\n",
|
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" <tr>\n",
|
||||
" <th>EK5730</th>\n",
|
||||
" <td>1741</td>\n",
|
||||
" <td>18.0</td>\n",
|
||||
" <td>25.0</td>\n",
|
||||
" <td>16.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EK9231</th>\n",
|
||||
" <td>1631</td>\n",
|
||||
" <td>37.0</td>\n",
|
||||
" <td>19.0</td>\n",
|
||||
" <td>21.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EH9899</th>\n",
|
||||
" <td>1570</td>\n",
|
||||
" <td>14.0</td>\n",
|
||||
" <td>36.0</td>\n",
|
||||
" <td>18.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN6205</th>\n",
|
||||
" <td>1487</td>\n",
|
||||
" <td>25.0</td>\n",
|
||||
" <td>37.0</td>\n",
|
||||
" <td>31.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN6208</th>\n",
|
||||
" <td>1475</td>\n",
|
||||
" <td>33.0</td>\n",
|
||||
" <td>27.0</td>\n",
|
||||
" <td>25.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>...</th>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN6266</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN626207</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN6262</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN6251</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>zw0151</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" </tbody>\n",
|
||||
"</table>\n",
|
||||
"<p>6765 rows × 4 columns</p>\n",
|
||||
"</div>"
|
||||
],
|
||||
"text/plain": [
|
||||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
|
||||
"VAX_LOT \n",
|
||||
"EK5730 1741 18.0 25.0 16.0\n",
|
||||
"EK9231 1631 37.0 19.0 21.0\n",
|
||||
"EH9899 1570 14.0 36.0 18.0\n",
|
||||
"EN6205 1487 25.0 37.0 31.0\n",
|
||||
"EN6208 1475 33.0 27.0 25.0\n",
|
||||
"... ... ... ... ...\n",
|
||||
"EN6266 1 0.0 0.0 0.0\n",
|
||||
"EN626207 1 0.0 0.0 0.0\n",
|
||||
"EN6262 1 0.0 0.0 0.0\n",
|
||||
"EN6251 1 0.0 0.0 0.0\n",
|
||||
"zw0151 1 0.0 1.0 0.0\n",
|
||||
"\n",
|
||||
"[6765 rows x 4 columns]"
|
||||
]
|
||||
},
|
||||
"metadata": {},
|
||||
"output_type": "display_data"
|
||||
},
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"'JANSSEN'"
|
||||
]
|
||||
},
|
||||
"metadata": {},
|
||||
"output_type": "display_data"
|
||||
},
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<div>\n",
|
||||
"<style scoped>\n",
|
||||
" .dataframe tbody tr th:only-of-type {\n",
|
||||
" vertical-align: middle;\n",
|
||||
" }\n",
|
||||
"\n",
|
||||
" .dataframe tbody tr th {\n",
|
||||
" vertical-align: top;\n",
|
||||
" }\n",
|
||||
"\n",
|
||||
" .dataframe thead th {\n",
|
||||
" text-align: right;\n",
|
||||
" }\n",
|
||||
"</style>\n",
|
||||
"<table border=\"1\" class=\"dataframe\">\n",
|
||||
" <thead>\n",
|
||||
" <tr style=\"text-align: right;\">\n",
|
||||
" <th></th>\n",
|
||||
" <th>ADRs</th>\n",
|
||||
" <th>DEATHS</th>\n",
|
||||
" <th>DISABILITIES</th>\n",
|
||||
" <th>LIFE THREATENING ILLNESSES</th>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>VAX_LOT</th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" </tr>\n",
|
||||
" </thead>\n",
|
||||
" <tbody>\n",
|
||||
" <tr>\n",
|
||||
" <th>043A21A</th>\n",
|
||||
" <td>1692</td>\n",
|
||||
" <td>28.0</td>\n",
|
||||
" <td>29.0</td>\n",
|
||||
" <td>37.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>042A21A</th>\n",
|
||||
" <td>1461</td>\n",
|
||||
" <td>43.0</td>\n",
|
||||
" <td>33.0</td>\n",
|
||||
" <td>35.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>202A21A</th>\n",
|
||||
" <td>1159</td>\n",
|
||||
" <td>22.0</td>\n",
|
||||
" <td>16.0</td>\n",
|
||||
" <td>21.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>1805018</th>\n",
|
||||
" <td>1129</td>\n",
|
||||
" <td>32.0</td>\n",
|
||||
" <td>30.0</td>\n",
|
||||
" <td>39.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>201A21A</th>\n",
|
||||
" <td>1129</td>\n",
|
||||
" <td>15.0</td>\n",
|
||||
" <td>27.0</td>\n",
|
||||
" <td>24.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>...</th>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>1808998</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>1808996</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>1808992</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>180898le</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>z03az1a</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" </tr>\n",
|
||||
" </tbody>\n",
|
||||
"</table>\n",
|
||||
"<p>1797 rows × 4 columns</p>\n",
|
||||
"</div>"
|
||||
],
|
||||
"text/plain": [
|
||||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
|
||||
"VAX_LOT \n",
|
||||
"043A21A 1692 28.0 29.0 37.0\n",
|
||||
"042A21A 1461 43.0 33.0 35.0\n",
|
||||
"202A21A 1159 22.0 16.0 21.0\n",
|
||||
"1805018 1129 32.0 30.0 39.0\n",
|
||||
"201A21A 1129 15.0 27.0 24.0\n",
|
||||
"... ... ... ... ...\n",
|
||||
"1808998 1 0.0 0.0 0.0\n",
|
||||
"1808996 1 0.0 0.0 0.0\n",
|
||||
"1808992 1 0.0 0.0 0.0\n",
|
||||
"180898le 1 0.0 0.0 0.0\n",
|
||||
"z03az1a 1 0.0 0.0 0.0\n",
|
||||
"\n",
|
||||
"[1797 rows x 4 columns]"
|
||||
]
|
||||
},
|
||||
"metadata": {},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"saveBatchCodeTable(\"MODERNA\", \"results/moderna.xlsx\")\n",
|
||||
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
|
||||
@@ -995,242 +524,26 @@
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 13,
|
||||
"execution_count": null,
|
||||
"id": "bc56831d",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"def saveSevereEffectsBatchCodeTable(excelFile):\n",
|
||||
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n",
|
||||
" DataFrameFilter.filterDataFrameForSevereEffects(\n",
|
||||
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||||
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
|
||||
" dose = '1'))\n",
|
||||
" vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n",
|
||||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
|
||||
" dataFrameFilter = DataFrameFilter(dataFrame)\n",
|
||||
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(dataFrameFilter.filterForSevereEffects(dose = '1'))\n",
|
||||
" display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",
|
||||
" severeEffectsBatchCodeTable.to_excel(excelFile)"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 14,
|
||||
"execution_count": null,
|
||||
"id": "ace3fed9",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"data": {
|
||||
"text/plain": [
|
||||
"'severeEffectsBatchCodeTable'"
|
||||
]
|
||||
},
|
||||
"metadata": {},
|
||||
"output_type": "display_data"
|
||||
},
|
||||
{
|
||||
"data": {
|
||||
"text/html": [
|
||||
"<div>\n",
|
||||
"<style scoped>\n",
|
||||
" .dataframe tbody tr th:only-of-type {\n",
|
||||
" vertical-align: middle;\n",
|
||||
" }\n",
|
||||
"\n",
|
||||
" .dataframe tbody tr th {\n",
|
||||
" vertical-align: top;\n",
|
||||
" }\n",
|
||||
"\n",
|
||||
" .dataframe thead th {\n",
|
||||
" text-align: right;\n",
|
||||
" }\n",
|
||||
"</style>\n",
|
||||
"<table border=\"1\" class=\"dataframe\">\n",
|
||||
" <thead>\n",
|
||||
" <tr style=\"text-align: right;\">\n",
|
||||
" <th></th>\n",
|
||||
" <th>ADRs</th>\n",
|
||||
" <th>DEATHS</th>\n",
|
||||
" <th>DISABILITIES</th>\n",
|
||||
" <th>LIFE THREATENING ILLNESSES</th>\n",
|
||||
" <th>HOSPITALISATIONS</th>\n",
|
||||
" <th>EMERGENCY ROOM OR DOCTOR VISITS</th>\n",
|
||||
" <th>COMPANY</th>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>VAX_LOT</th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" <th></th>\n",
|
||||
" </tr>\n",
|
||||
" </thead>\n",
|
||||
" <tbody>\n",
|
||||
" <tr>\n",
|
||||
" <th>026L20A</th>\n",
|
||||
" <td>3335</td>\n",
|
||||
" <td>25.0</td>\n",
|
||||
" <td>24.0</td>\n",
|
||||
" <td>21.0</td>\n",
|
||||
" <td>125.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>039K20A</th>\n",
|
||||
" <td>3335</td>\n",
|
||||
" <td>67.0</td>\n",
|
||||
" <td>22.0</td>\n",
|
||||
" <td>29.0</td>\n",
|
||||
" <td>134.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>011J20A</th>\n",
|
||||
" <td>3078</td>\n",
|
||||
" <td>34.0</td>\n",
|
||||
" <td>27.0</td>\n",
|
||||
" <td>26.0</td>\n",
|
||||
" <td>106.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>025L20A</th>\n",
|
||||
" <td>2397</td>\n",
|
||||
" <td>42.0</td>\n",
|
||||
" <td>16.0</td>\n",
|
||||
" <td>26.0</td>\n",
|
||||
" <td>83.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>012L20A</th>\n",
|
||||
" <td>2357</td>\n",
|
||||
" <td>57.0</td>\n",
|
||||
" <td>29.0</td>\n",
|
||||
" <td>22.0</td>\n",
|
||||
" <td>135.0</td>\n",
|
||||
" <td>1.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>...</th>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" <td>...</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>EN6207-</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>PFIZER\\BIONTECH</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>039820A</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>Blue-218</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>MODERNA</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>1808973</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>UNKNOWN MANUFACTURER</td>\n",
|
||||
" </tr>\n",
|
||||
" <tr>\n",
|
||||
" <th>FJ1161</th>\n",
|
||||
" <td>1</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>0.0</td>\n",
|
||||
" <td>PFIZER\\BIONTECH</td>\n",
|
||||
" </tr>\n",
|
||||
" </tbody>\n",
|
||||
"</table>\n",
|
||||
"<p>18428 rows × 7 columns</p>\n",
|
||||
"</div>"
|
||||
],
|
||||
"text/plain": [
|
||||
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES \\\n",
|
||||
"VAX_LOT \n",
|
||||
"026L20A 3335 25.0 24.0 21.0 \n",
|
||||
"039K20A 3335 67.0 22.0 29.0 \n",
|
||||
"011J20A 3078 34.0 27.0 26.0 \n",
|
||||
"025L20A 2397 42.0 16.0 26.0 \n",
|
||||
"012L20A 2357 57.0 29.0 22.0 \n",
|
||||
"... ... ... ... ... \n",
|
||||
"EN6207- 1 0.0 0.0 0.0 \n",
|
||||
"039820A 1 0.0 0.0 0.0 \n",
|
||||
"Blue-218 1 0.0 0.0 0.0 \n",
|
||||
"1808973 1 0.0 0.0 0.0 \n",
|
||||
"FJ1161 1 0.0 0.0 0.0 \n",
|
||||
"\n",
|
||||
" HOSPITALISATIONS EMERGENCY ROOM OR DOCTOR VISITS \\\n",
|
||||
"VAX_LOT \n",
|
||||
"026L20A 125.0 0.0 \n",
|
||||
"039K20A 134.0 0.0 \n",
|
||||
"011J20A 106.0 0.0 \n",
|
||||
"025L20A 83.0 0.0 \n",
|
||||
"012L20A 135.0 1.0 \n",
|
||||
"... ... ... \n",
|
||||
"EN6207- 0.0 0.0 \n",
|
||||
"039820A 0.0 0.0 \n",
|
||||
"Blue-218 0.0 0.0 \n",
|
||||
"1808973 0.0 0.0 \n",
|
||||
"FJ1161 0.0 0.0 \n",
|
||||
"\n",
|
||||
" COMPANY \n",
|
||||
"VAX_LOT \n",
|
||||
"026L20A MODERNA \n",
|
||||
"039K20A MODERNA \n",
|
||||
"011J20A MODERNA \n",
|
||||
"025L20A MODERNA \n",
|
||||
"012L20A MODERNA \n",
|
||||
"... ... \n",
|
||||
"EN6207- PFIZER\\BIONTECH \n",
|
||||
"039820A MODERNA \n",
|
||||
"Blue-218 MODERNA \n",
|
||||
"1808973 UNKNOWN MANUFACTURER \n",
|
||||
"FJ1161 PFIZER\\BIONTECH \n",
|
||||
"\n",
|
||||
"[18428 rows x 7 columns]"
|
||||
]
|
||||
},
|
||||
"metadata": {},
|
||||
"output_type": "display_data"
|
||||
}
|
||||
],
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"saveSevereEffectsBatchCodeTable('results/severeEffects.xlsx')"
|
||||
]
|
||||
|
||||
Reference in New Issue
Block a user