francois/HowBadIsMyBatch
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refactoring

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frankknoll
2022-02-01 08:43:53 +01:00
parent b025bf2aae
commit b97d95d28f
1 changed files with 26 additions and 20 deletions
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46
HowBadIsMyBatch.ipynb
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@@ -65,18 +65,24 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"def createDataFrameFromDescr(vaersDescr):\n", "import pandas as pd\n",
" return pd.merge(\n",
" vaersDescr['VAERSDATA'],\n",
" vaersDescr['VAERSVAX'],\n",
" how = 'left',\n",
" left_index = True,\n",
" right_index = True,\n",
" validate = 'one_to_many')\n",
"\n", "\n",
"def createDataFrameFromDescrs(vaersDescrs):\n", "class VaersDescr2DataFrameConverter:\n",
" dataFrames = [createDataFrameFromDescr(vaersDescr) for vaersDescr in vaersDescrs]\n", "\n",
" return pd.concat(dataFrames)\n" " @staticmethod\n",
" def createDataFrameFromDescr(vaersDescr):\n",
" return pd.merge(\n",
" vaersDescr['VAERSDATA'],\n",
" vaersDescr['VAERSVAX'],\n",
" how = 'left',\n",
" left_index = True,\n",
" right_index = True,\n",
" validate = 'one_to_many')\n",
"\n",
" @staticmethod\n",
" def createDataFrameFromDescrs(vaersDescrs):\n",
" dataFrames = [VaersDescr2DataFrameConverter.createDataFrameFromDescr(vaersDescr) for vaersDescr in vaersDescrs]\n",
" return pd.concat(dataFrames)\n"
] ]
}, },
{ {
@@ -209,7 +215,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]\n", " ]\n",
" dataFrame = createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n", " dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
@@ -248,7 +254,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]\n", " ]\n",
" dataFrame = createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = filterDataFrameForSevereEffects(dataFrame, dose = '1')\n", " dataFrame = filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
@@ -283,7 +289,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]\n", " ]\n",
" dataFrame = createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n", " dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
@@ -316,7 +322,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n", " }\n",
" ]\n", " ]\n",
" dataFrame = createDataFrameFromDescrs(vaersDescrs)\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n", " dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
@@ -346,7 +352,7 @@
"class BatchCodeTableTest(unittest.TestCase):\n", "class BatchCodeTableTest(unittest.TestCase):\n",
"\n", "\n",
" def test_createBatchCodeTable2(self):\n", " def test_createBatchCodeTable2(self):\n",
" dataFrame = createDataFrameFromDescrs(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -389,7 +395,7 @@
" def test_createBatchCodeTable(self):\n", " def test_createBatchCodeTable(self):\n",
" self._test_createBatchCodeTable(\n", " self._test_createBatchCodeTable(\n",
" filterDataFrame(\n", " filterDataFrame(\n",
" createDataFrameFromDescrs(\n", " VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(\"test/VAERS\").readAllVaersDescrs()),\n", " VaersDescrReader(\"test/VAERS\").readAllVaersDescrs()),\n",
" manufacturer = \"MODERNA\",\n", " manufacturer = \"MODERNA\",\n",
" dose = '1'))\n", " dose = '1'))\n",
@@ -426,7 +432,7 @@
"\n", "\n",
" def test_createSevereEffectsBatchCodeTable(self):\n", " def test_createSevereEffectsBatchCodeTable(self):\n",
" # Given\n", " # Given\n",
" dataFrame = createDataFrameFromDescrs(\n", " dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -490,7 +496,7 @@
"def saveBatchCodeTable(manufacturer, excelFile):\n", "def saveBatchCodeTable(manufacturer, excelFile):\n",
" batchCodeTable = createBatchCodeTable(\n", " batchCodeTable = createBatchCodeTable(\n",
" filterDataFrame(\n", " filterDataFrame(\n",
" createDataFrameFromDescrs(\n", " VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n", " VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
" manufacturer = manufacturer,\n", " manufacturer = manufacturer,\n",
" dose = '1'))\n", " dose = '1'))\n",
@@ -520,7 +526,7 @@
"def saveSevereEffectsBatchCodeTable(excelFile):\n", "def saveSevereEffectsBatchCodeTable(excelFile):\n",
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n", " severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n",
" filterDataFrameForSevereEffects(\n", " filterDataFrameForSevereEffects(\n",
" createDataFrameFromDescrs(\n", " VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n", " VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
" dose = '1'))\n", " dose = '1'))\n",
" display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n", " display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",