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refactoring

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This commit is contained in:
frankknoll
2022-02-01 09:43:20 +01:00
parent 573c6038b2
commit 87ce4ac013
1 changed files with 29 additions and 717 deletions
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746
HowBadIsMyBatch.ipynb
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@@ -2,7 +2,7 @@
"cells": [ "cells": [
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 21, "execution_count": null,
"id": "9de5907f-18f5-4cb1-903e-26028ff1fa03", "id": "9de5907f-18f5-4cb1-903e-26028ff1fa03",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -16,7 +16,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 22, "execution_count": null,
"id": "a271254b", "id": "a271254b",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -61,7 +61,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 23, "execution_count": null,
"id": "7b5d6df0", "id": "7b5d6df0",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -88,7 +88,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 24, "execution_count": null,
"id": "3ebcba86", "id": "3ebcba86",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -118,7 +118,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 25, "execution_count": null,
"id": "99945ca8", "id": "99945ca8",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -129,14 +129,11 @@
" \n", " \n",
" @staticmethod\n", " @staticmethod\n",
" def createBatchCodeTable(df : pd.DataFrame):\n", " def createBatchCodeTable(df : pd.DataFrame):\n",
" def filterDataFrame(df, col):\n",
" return df[df[col] == 'Y']['VAX_LOT']\n",
"\n",
" batchCodeTableDict = {\n", " batchCodeTableDict = {\n",
" 'ADRs': df['VAX_LOT'].value_counts(),\n", " 'ADRs': df['VAX_LOT'].value_counts(),\n",
" 'DEATHS': filterDataFrame(df, 'DIED').value_counts(),\n", " 'DEATHS': BatchCodeTableFactory._filterDataFrame(df, 'DIED').value_counts(),\n",
" 'DISABILITIES': filterDataFrame(df, 'DISABLE').value_counts(),\n", " 'DISABILITIES': BatchCodeTableFactory._filterDataFrame(df, 'DISABLE').value_counts(),\n",
" 'LIFE THREATENING ILLNESSES': filterDataFrame(df, 'L_THREAT').value_counts()\n", " 'LIFE THREATENING ILLNESSES': BatchCodeTableFactory._filterDataFrame(df, 'L_THREAT').value_counts()\n",
" }\n", " }\n",
" batchCodeTable = pd.concat(batchCodeTableDict, axis = 'columns')\n", " batchCodeTable = pd.concat(batchCodeTableDict, axis = 'columns')\n",
" batchCodeTable.index.name = 'VAX_LOT'\n", " batchCodeTable.index.name = 'VAX_LOT'\n",
@@ -146,16 +143,13 @@
" # FK-TODO: DRY with createBatchCodeTable()\n", " # FK-TODO: DRY with createBatchCodeTable()\n",
" @staticmethod\n", " @staticmethod\n",
" def createSevereEffectsBatchCodeTable(df : pd.DataFrame):\n", " def createSevereEffectsBatchCodeTable(df : pd.DataFrame):\n",
" def filterDataFrame(df, col):\n",
" return df[df[col] == 'Y']['VAX_LOT']\n",
"\n",
" batchCodeTableDict = {\n", " batchCodeTableDict = {\n",
" 'ADRs': df['VAX_LOT'].value_counts(),\n", " 'ADRs': df['VAX_LOT'].value_counts(),\n",
" 'DEATHS': filterDataFrame(df, 'DIED').value_counts(),\n", " 'DEATHS': BatchCodeTableFactory._filterDataFrame(df, 'DIED').value_counts(),\n",
" 'DISABILITIES': filterDataFrame(df, 'DISABLE').value_counts(),\n", " 'DISABILITIES': BatchCodeTableFactory._filterDataFrame(df, 'DISABLE').value_counts(),\n",
" 'LIFE THREATENING ILLNESSES': filterDataFrame(df, 'L_THREAT').value_counts(),\n", " 'LIFE THREATENING ILLNESSES': BatchCodeTableFactory._filterDataFrame(df, 'L_THREAT').value_counts(),\n",
" 'HOSPITALISATIONS': filterDataFrame(df, 'HOSPITAL').value_counts(),\n", " 'HOSPITALISATIONS': BatchCodeTableFactory._filterDataFrame(df, 'HOSPITAL').value_counts(),\n",
" 'EMERGENCY ROOM OR DOCTOR VISITS': filterDataFrame(df, 'ER_VISIT').value_counts()\n", " 'EMERGENCY ROOM OR DOCTOR VISITS': BatchCodeTableFactory._filterDataFrame(df, 'ER_VISIT').value_counts()\n",
" }\n", " }\n",
" batchCodeTable = pd.concat(batchCodeTableDict, axis = 'columns')\n", " batchCodeTable = pd.concat(batchCodeTableDict, axis = 'columns')\n",
" batchCodeTable.index.name = 'VAX_LOT'\n", " batchCodeTable.index.name = 'VAX_LOT'\n",
@@ -170,6 +164,10 @@
" return batchCodeTable.replace(to_replace = np.nan, value = 0)\n", " return batchCodeTable.replace(to_replace = np.nan, value = 0)\n",
"\n", "\n",
" @staticmethod\n", " @staticmethod\n",
" def _filterDataFrame(df, col):\n",
" return df[df[col] == 'Y']['VAX_LOT']\n",
"\n",
" @staticmethod\n",
" def _createManufacturerByBatchCodeTable(df):\n", " def _createManufacturerByBatchCodeTable(df):\n",
" manufacturerByBatchCodeTable = df[['VAX_LOT', 'VAX_MANU']]\n", " manufacturerByBatchCodeTable = df[['VAX_LOT', 'VAX_MANU']]\n",
" manufacturerByBatchCodeTable = manufacturerByBatchCodeTable.drop_duplicates(subset = ['VAX_LOT'])\n", " manufacturerByBatchCodeTable = manufacturerByBatchCodeTable.drop_duplicates(subset = ['VAX_LOT'])\n",
@@ -182,7 +180,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 26, "execution_count": null,
"id": "3dacedfd", "id": "3dacedfd",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -192,7 +190,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 27, "execution_count": null,
"id": "e59a1825", "id": "e59a1825",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -366,7 +364,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 28, "execution_count": null,
"id": "e14465d7", "id": "e14465d7",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -445,7 +443,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 29, "execution_count": null,
"id": "ded70c87", "id": "ded70c87",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -502,46 +500,17 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 30, "execution_count": null,
"id": "5a8bff1b", "id": "5a8bff1b",
"metadata": {}, "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 0.143s\n",
"\n",
"OK\n"
]
},
{
"data": {
"text/plain": [
"<unittest.main.TestProgram at 0x7f63c8007580>"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [ "source": [
"unittest.main(argv = [''], verbosity = 2, exit = False)" "unittest.main(argv = [''], verbosity = 2, exit = False)"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 32, "execution_count": null,
"id": "86e0e4f2", "id": "86e0e4f2",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -557,452 +526,10 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 33, "execution_count": null,
"id": "ab170c16", "id": "ab170c16",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [],
{
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"'MODERNA'"
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" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
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"... ... ... ... ...\n",
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"\n",
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" ADRs DEATHS DISABILITIES LIFE THREATENING ILLNESSES\n",
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},
"metadata": {},
"output_type": "display_data"
}
],
"source": [ "source": [
"saveBatchCodeTable(\"MODERNA\", \"results/moderna.xlsx\")\n", "saveBatchCodeTable(\"MODERNA\", \"results/moderna.xlsx\")\n",
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n", "saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
@@ -1011,7 +538,7 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 34, "execution_count": null,
"id": "bc56831d", "id": "bc56831d",
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
@@ -1027,225 +554,10 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": 35, "execution_count": null,
"id": "ace3fed9", "id": "ace3fed9",
"metadata": {}, "metadata": {},
"outputs": [ "outputs": [],
{
"data": {
"text/plain": [
"'severeEffectsBatchCodeTable'"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
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"<div>\n",
"<style scoped>\n",
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" .dataframe thead th {\n",
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"</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",
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" <th>039K20A</th>\n",
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" <th>012L20A</th>\n",
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" <tr>\n",
" <th>...</th>\n",
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" <tr>\n",
" <th>1808973</th>\n",
" <td>1</td>\n",
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" <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",
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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": [ "source": [
"saveSevereEffectsBatchCodeTable('results/severeEffects.xlsx')" "saveSevereEffectsBatchCodeTable('results/severeEffects.xlsx')"
] ]