francois/HowBadIsMyBatch
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

refactoring

Browse Source
This commit is contained in:
frankknoll
2022-01-31 21:38:06 +01:00
parent 61f8e97cde
commit b812b6fc0b
1 changed files with 17 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files

31
HowBadIsMyBatch.ipynb
View File

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