refactoring

This commit is contained in:
frankknoll
2022-02-01 08:51:55 +01:00
parent b97d95d28f
commit ac2deaef81

View File

@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "9de5907f-18f5-4cb1-903e-26028ff1fa03",
"metadata": {},
"outputs": [],
@@ -16,7 +16,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"id": "a271254b",
"metadata": {},
"outputs": [],
@@ -60,7 +60,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"id": "7b5d6df0",
"metadata": {},
"outputs": [],
@@ -87,24 +87,30 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"id": "3ebcba86",
"metadata": {},
"outputs": [],
"source": [
"def filterDataFrame(df, manufacturer = None, dose = None):\n",
" isCovid19 = df[\"VAX_TYPE\"] == \"COVID19\"\n",
" isManufacturer = df[\"VAX_MANU\"] == manufacturer if manufacturer 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",
"import pandas as pd\n",
"\n",
"def filterDataFrameForSevereEffects(df, dose):\n",
" return filterDataFrame(df, dose = dose)\n"
"class DataFrameFilter:\n",
" \n",
" @staticmethod\n",
" def filterDataFrame(df, manufacturer = None, dose = None):\n",
" isCovid19 = df[\"VAX_TYPE\"] == \"COVID19\"\n",
" isManufacturer = df[\"VAX_MANU\"] == manufacturer if manufacturer 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",
"\n",
" @staticmethod\n",
" def filterDataFrameForSevereEffects(df, dose):\n",
" return DataFrameFilter.filterDataFrame(df, dose = dose)\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"id": "99945ca8",
"metadata": {},
"outputs": [],
@@ -158,7 +164,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"id": "3dacedfd",
"metadata": {},
"outputs": [],
@@ -168,7 +174,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"id": "e59a1825",
"metadata": {},
"outputs": [],
@@ -218,7 +224,7 @@
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n",
" # When\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" \n",
" # Then\n",
" dataFrameExpected = self.createDataFrame(\n",
@@ -257,7 +263,7 @@
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n",
" # When\n",
" dataFrame = filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
" dataFrame = DataFrameFilter.filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
" \n",
" # Then\n",
" dataFrameExpected = self.createDataFrame(\n",
@@ -292,7 +298,7 @@
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n",
" # When\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" \n",
" # Then\n",
" dataFrameExpected = self.createDataFrame(\n",
@@ -325,7 +331,7 @@
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
" \n",
" # When\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
" \n",
" # Then\n",
" dataFrameExpected = self.createDataFrame(\n",
@@ -342,7 +348,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"id": "e14465d7",
"metadata": {},
"outputs": [],
@@ -389,12 +395,12 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" }\n",
" ])\n",
" dataFrame = filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" dataFrame = DataFrameFilter.filterDataFrame(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
" self._test_createBatchCodeTable(dataFrame);\n",
"\n",
" def test_createBatchCodeTable(self):\n",
" self._test_createBatchCodeTable(\n",
" filterDataFrame(\n",
" DataFrameFilter.filterDataFrame(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(\"test/VAERS\").readAllVaersDescrs()),\n",
" manufacturer = \"MODERNA\",\n",
@@ -421,7 +427,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"id": "ded70c87",
"metadata": {},
"outputs": [],
@@ -453,7 +459,7 @@
" }\n",
" ]\n",
" )\n",
" dataFrame = filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
" dataFrame = DataFrameFilter.filterDataFrameForSevereEffects(dataFrame, dose = '1')\n",
"\n",
" # When\n",
" batchCodeTable = createSevereEffectsBatchCodeTable(dataFrame)\n",
@@ -478,24 +484,53 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 10,
"id": "5a8bff1b",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"test_createBatchCodeTable (__main__.BatchCodeTableTest) ... ok\n",
"test_createBatchCodeTable2 (__main__.BatchCodeTableTest) ... ok\n",
"test_createAndFilterDataFrameFromDescrs (__main__.CreateAndFilterDataFrameTest) ... ok\n",
"test_createAndFilterDataFrameFromDescrsWithFirstDose (__main__.CreateAndFilterDataFrameTest) ... ok\n",
"test_createAndFilterDataFrameFromDescrsWithSecondDose (__main__.CreateAndFilterDataFrameTest) ... ok\n",
"test_createDataFrameFromForSevereEffects (__main__.CreateAndFilterDataFrameTest) ... ok\n",
"test_createSevereEffectsBatchCodeTable (__main__.SevereEffectsBatchCodeTableTest) ... ok\n",
"\n",
"----------------------------------------------------------------------\n",
"Ran 7 tests in 0.156s\n",
"\n",
"OK\n"
]
},
{
"data": {
"text/plain": [
"<unittest.main.TestProgram at 0x7f8aa7824220>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"unittest.main(argv = [''], verbosity = 2, exit = False)"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 11,
"id": "86e0e4f2",
"metadata": {},
"outputs": [],
"source": [
"def saveBatchCodeTable(manufacturer, excelFile):\n",
" batchCodeTable = createBatchCodeTable(\n",
" filterDataFrame(\n",
" DataFrameFilter.filterDataFrame(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
" manufacturer = manufacturer,\n",
@@ -506,10 +541,452 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 12,
"id": "ab170c16",
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"'MODERNA'"
]
},
"metadata": {},
"output_type": "display_data"
},
{
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],
"text/plain": [
" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
"VAX_LOT \n",
"039K20A 3330 67.0 22.0 29.0\n",
"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",
"\n",
"[10248 rows x 4 columns]"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"text/plain": [
"'PFIZER\\\\BIONTECH'"
]
},
"metadata": {},
"output_type": "display_data"
},
{
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" <th>VAX_LOT</th>\n",
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],
"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",
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"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"
},
{
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],
"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",
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"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"
}
],
"source": [
"saveBatchCodeTable(\"MODERNA\", \"results/moderna.xlsx\")\n",
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
@@ -518,14 +995,14 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 13,
"id": "bc56831d",
"metadata": {},
"outputs": [],
"source": [
"def saveSevereEffectsBatchCodeTable(excelFile):\n",
" severeEffectsBatchCodeTable = createSevereEffectsBatchCodeTable(\n",
" filterDataFrameForSevereEffects(\n",
" DataFrameFilter.filterDataFrameForSevereEffects(\n",
" VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
" VaersDescrReader(\"VAERS\").readAllVaersDescrs()),\n",
" dose = '1'))\n",
@@ -535,10 +1012,225 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 14,
"id": "ace3fed9",
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"'severeEffectsBatchCodeTable'"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
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"<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",
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" <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",
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" <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",
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" <th>039820A</th>\n",
" <td>1</td>\n",
" <td>0.0</td>\n",
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" <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",
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" </tr>\n",
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"</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"
}
],
"source": [
"saveSevereEffectsBatchCodeTable('results/severeEffects.xlsx')"
]