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refactoring

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frankknoll
2022-01-28 17:41:05 +01:00
parent 906ec737ec
commit 72c99fae06
1 changed files with 27 additions and 46 deletions
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73
HowBadIsMyBatch.ipynb
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@@ -17,34 +17,11 @@
{
"cell_type": "code",
"execution_count": null,
"id": "233bc590",
"id": "7b5d6df0",
"metadata": {},
"outputs": [],
"source": [
"def createDataFrame(dataDir, manufacturer):\n",
" def read_csv(file, usecols):\n",
" return pd.read_csv(file, index_col = 'VAERS_ID', encoding = 'latin1', low_memory = False, usecols = usecols)\n",
"\n",
" def createDataFrameForYear(year):\n",
" folder = dataDir + \"/\" + year + \"VAERSData/\"\n",
" return pd.merge(\n",
" read_csv(folder + year + \"VAERSDATA.csv\", ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE']),\n",
" read_csv(folder + year + \"VAERSVAX.csv\", ['VAERS_ID', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT']),\n",
" left_index = True,\n",
" right_index = True)\n",
"\n",
" df = pd.concat([createDataFrameForYear(\"2021\"), createDataFrameForYear(\"2022\")])\n",
" return df[(df[\"VAX_TYPE\"] == \"COVID19\") & (df[\"VAX_MANU\"] == manufacturer)]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "dea776cd",
"metadata": {},
"outputs": [],
"source": [
"def createDataFrame2(vaersDescrs, manufacturer):\n",
"def _createDataFrame(vaersDescrs, manufacturer):\n",
" def vaersDescr2Vaers(vaersDescr):\n",
" return pd.merge(vaersDescr['VAERSDATA'], vaersDescr['VAERSVAX'], left_index = True, right_index = True)\n",
"\n",
@@ -55,6 +32,29 @@
" return df[(df[\"VAX_TYPE\"] == \"COVID19\") & (df[\"VAX_MANU\"] == manufacturer)]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "233bc590",
"metadata": {},
"outputs": [],
"source": [
"def read_csv(file, usecols):\n",
" return pd.read_csv(file, index_col = 'VAERS_ID', encoding = 'latin1', low_memory = False, usecols = usecols)\n",
"\n",
"def readVaersDescr(dataDir, year):\n",
" folder = dataDir + \"/\" + year + \"VAERSData/\"\n",
" return {\n",
" 'VAERSDATA': read_csv(folder + year + \"VAERSDATA.csv\", ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE']),\n",
" 'VAERSVAX': read_csv(folder + year + \"VAERSVAX.csv\", ['VAERS_ID', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'])\n",
" }\n",
"\n",
"def createDataFrame(dataDir, manufacturer):\n",
" return _createDataFrame(\n",
" [readVaersDescr(dataDir, \"2021\"), readVaersDescr(dataDir, \"2022\")],\n",
" manufacturer)"
]
},
{
"cell_type": "code",
"execution_count": null,
@@ -97,7 +97,6 @@
"class BatchCodeTableTest(unittest.TestCase):\n",
"\n",
" def test_createBatchCodeTable2(self):\n",
" # Given\n",
" vaersData2021 = pd.DataFrame(columns = ['DIED', 'L_THREAT', 'DISABLE'], index = ['0916600', '0916601'])\n",
" vaersData2021.loc['0916600'] = pd.Series({'DIED': 'Y', 'L_THREAT': np.NaN, 'DISABLE': np.NaN})\n",
" vaersData2021.loc['0916601'] = pd.Series({'DIED': np.NaN, 'L_THREAT': np.NaN, 'DISABLE': 'Y'})\n",
@@ -114,28 +113,21 @@
" vaersVax2022.loc['1996873'] = pd.Series({'VAX_TYPE': 'HPV9', 'VAX_MANU': 'MERCK & CO. INC.', 'VAX_LOT': 'R017624'})\n",
" vaersVax2022.loc['1996874'] = pd.Series({'VAX_TYPE': 'COVID19', 'VAX_MANU': 'MODERNA', 'VAX_LOT': '025L20A'})\n",
" \n",
" dataFrame = createDataFrame2(\n",
" dataFrame = _createDataFrame(\n",
" [\n",
" {'VAERSDATA': vaersData2021, 'VAERSVAX': vaersVax2021},\n",
" {'VAERSDATA': vaersData2022, 'VAERSVAX': vaersVax2022}\n",
" ],\n",
" \"MODERNA\")\n",
" display(\"dataFrame:\", dataFrame)\n",
"\n",
" # When\n",
" self._test_createBatchCodeTable(dataFrame);\n",
" \n",
" def test_createBatchCodeTable(self):\n",
" # Given\n",
" dataFrame = createDataFrame(\"test/VAERS\", \"MODERNA\")\n",
" display(\"dataFrame:\", dataFrame)\n",
" self._test_createBatchCodeTable(dataFrame);\n",
"\n",
" self._test_createBatchCodeTable(createDataFrame(\"test/VAERS\", \"MODERNA\"));\n",
"\n",
" def _test_createBatchCodeTable(self, dataFrame):\n",
" # When\n",
" batchCodeTable = createBatchCodeTable(dataFrame)\n",
" display(\"batchCodeTable:\", batchCodeTable)\n",
"\n",
" # Then\n",
" batchCodeTableExpected = pd.DataFrame(\n",
@@ -146,7 +138,6 @@
" 'LIFE THREATENING ILLNESSES': [0, 0]\n",
" },\n",
" index = pd.MultiIndex.from_arrays([['025L20A', '037K20A']], names = ('VAX_LOT',)))\n",
" display(\"batchCodeTableExpected:\", batchCodeTableExpected)\n",
" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n",
"\n",
" "
@@ -186,16 +177,6 @@
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
"saveBatchCodeTable(\"JANSSEN\", \"results/janssen.xlsx\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ef8f99c4",
"metadata": {},
"outputs": [],
"source": [
"unittest.main(argv = [''], verbosity = 2, exit = False)"
]
}
],
"metadata": {