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refactoring

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frankknoll
2022-01-31 21:38:06 +01:00
parent 61f8e97cde
commit b812b6fc0b
1 changed files with 17 additions and 14 deletions
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31
HowBadIsMyBatch.ipynb
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@@ -85,14 +85,12 @@
" isDose = df[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n",
" return df[isCovid19 & isManufacturer & isDose]\n",
"\n",
"# FK-TODO: inline method\n",
"def createAndFilterDataFrameFromDescrs(vaersDescrs, manufacturer, dose):\n",
" return filterDataFrame(createDataFrameFromDescrs(vaersDescrs), manufacturer = manufacturer, dose = dose)\n",
"\n",
"def filterDataFrameForSevereEffects(df, dose):\n",
" return filterDataFrame(df, dose = dose)\n",
"\n",
"def createDataFrameSevereEffectsFromDescrs(vaersDescrs, dose):\n",
" return filterDataFrameForSevereEffects(createDataFrameFromDescrs(vaersDescrs), dose = dose)"
" return filterDataFrame(df, dose = dose)\n"
]
},
{
@@ -102,11 +100,9 @@
"metadata": {},
"outputs": [],
"source": [
"# FK-TODO: inline method\n",
"def createAndFilterDataFrameFromFiles(dataDir, manufacturer, dose):\n",
" return createAndFilterDataFrameFromDescrs(readAllVaersDescrs(dataDir), manufacturer, dose)\n",
"\n",
"def createDataFrameSevereEffectsFromFiles(dataDir, dose):\n",
" return createDataFrameSevereEffectsFromDescrs(readAllVaersDescrs(dataDir), dose)"
" return createAndFilterDataFrameFromDescrs(readAllVaersDescrs(dataDir), manufacturer, dose)\n"
]
},
{
@@ -258,9 +254,10 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n",
" ]\n",
" \n",
" dataFrame = createDataFrameFromDescrs(vaersDescrs)\n",
" \n",
" # When\n",
" dataFrame = createDataFrameSevereEffectsFromDescrs(vaersDescrs, '1')\n",
" dataFrame = filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
" \n",
" # Then\n",
" dataFrameExpected = self.createDataFrame(\n",
@@ -429,7 +426,8 @@
"class SevereEffectsBatchCodeTableTest(unittest.TestCase):\n",
"\n",
" def test_createSevereEffectsBatchCodeTable(self):\n",
" dataFrame = createDataFrameSevereEffectsFromDescrs(\n",
" # Given\n",
" dataFrame = createDataFrameFromDescrs(\n",
" [\n",
" {\n",
" 'VAERSDATA': self.createDataFrame(\n",
@@ -448,8 +446,9 @@
" \"0916601\"],\n",
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n",
" ],\n",
" '1')\n",
" ]\n",
" )\n",
" dataFrame = filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
"\n",
" # When\n",
" batchCodeTable = createSevereEffectsBatchCodeTable(dataFrame)\n",
@@ -515,7 +514,11 @@
"outputs": [],
"source": [
"def saveSevereEffectsBatchCodeTable(excelFile):\n",
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(createDataFrameSevereEffectsFromFiles(\"VAERS\", '1'))\n",
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n",
" filterDataFrameForSevereEffects(\n",
" createDataFrameFromDescrs(\n",
" readAllVaersDescrs(\"VAERS\")),\n",
" dose = '1'))\n",
" display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",
" severeEffectsBatchCodeTable.to_excel(excelFile)"
]