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refactoring

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frankknoll
2022-01-29 02:52:28 +01:00
parent 05e70ffbc5
commit 6702d8456d
1 changed files with 18 additions and 19 deletions
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37
HowBadIsMyBatch.ipynb
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@@ -21,7 +21,7 @@
"metadata": {}, "metadata": {},
"outputs": [], "outputs": [],
"source": [ "source": [
"def _createDataFrame(vaersDescrs, manufacturer, dose):\n", "def createDataFrameFromDescrs(vaersDescrs, manufacturer, dose):\n",
" def filter(df):\n", " def filter(df):\n",
" return df[\n", " return df[\n",
" (df[\"VAX_TYPE\"] == \"COVID19\") &\n", " (df[\"VAX_TYPE\"] == \"COVID19\") &\n",
@@ -58,11 +58,18 @@
"\n", "\n",
" folder = dataDir + \"/\" + year + \"VAERSData/\"\n", " folder = dataDir + \"/\" + year + \"VAERSData/\"\n",
" return {\n", " return {\n",
" 'VAERSDATA': read_csv(folder + year + \"VAERSDATA.csv\", ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE']),\n", " 'VAERSDATA':\n",
" 'VAERSVAX': read_csv(folder + year + \"VAERSVAX.csv\", ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'], dtype = {\"VAX_DOSE_SERIES\": \"string\"})\n", " read_csv(\n",
" folder + year + \"VAERSDATA.csv\",\n",
" ['VAERS_ID', 'DIED', 'L_THREAT', 'DISABLE']),\n",
" 'VAERSVAX':\n",
" read_csv(\n",
" folder + year + \"VAERSVAX.csv\",\n",
" ['VAERS_ID', 'VAX_DOSE_SERIES', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT'],\n",
" dtype = {\"VAX_DOSE_SERIES\": \"string\"})\n",
" }\n", " }\n",
"\n", "\n",
" return _createDataFrame(\n", " return createDataFrameFromDescrs(\n",
" [readVaersDescr(\"2021\"), readVaersDescr(\"2022\")],\n", " [readVaersDescr(\"2021\"), readVaersDescr(\"2022\")],\n",
" manufacturer,\n", " manufacturer,\n",
" dose)" " dose)"
@@ -108,7 +115,7 @@
"\n", "\n",
"class CreateDataFrameTest(unittest.TestCase):\n", "class CreateDataFrameTest(unittest.TestCase):\n",
"\n", "\n",
" def test_createDataFrame(self):\n", " def test_createDataFrameFromDescrs(self):\n",
" # Given\n", " # Given\n",
" vaersDescrs = [\n", " vaersDescrs = [\n",
" {\n", " {\n",
@@ -140,7 +147,7 @@
" ]\n", " ]\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = _createDataFrame(vaersDescrs, \"MODERNA\", '1')\n", " dataFrame = createDataFrameFromDescrs(vaersDescrs, \"MODERNA\", '1')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -152,7 +159,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n", " assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
"\n", "\n",
" def test_createDataFrameWithFirstDose(self):\n", " def test_createDataFrameFromDescrsWithFirstDose(self):\n",
" # Given\n", " # Given\n",
" vaersDescrs = [\n", " vaersDescrs = [\n",
" {\n", " {\n",
@@ -170,7 +177,7 @@
" ]\n", " ]\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = _createDataFrame(vaersDescrs, \"MODERNA\", '1')\n", " dataFrame = createDataFrameFromDescrs(vaersDescrs, \"MODERNA\", '1')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -180,7 +187,7 @@
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n", " dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n", " assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
"\n", "\n",
" def test_createDataFrameWithSecondDose(self):\n", " def test_createDataFrameFromDescrsWithSecondDose(self):\n",
" # Given\n", " # Given\n",
" vaersDescrs = [\n", " vaersDescrs = [\n",
" {\n", " {\n",
@@ -198,7 +205,7 @@
" ]\n", " ]\n",
" \n", " \n",
" # When\n", " # When\n",
" dataFrame = _createDataFrame(vaersDescrs, \"MODERNA\", '2')\n", " dataFrame = createDataFrameFromDescrs(vaersDescrs, \"MODERNA\", '2')\n",
" \n", " \n",
" # Then\n", " # Then\n",
" dataFrameExpected = self.createDataFrame(\n", " dataFrameExpected = self.createDataFrame(\n",
@@ -224,7 +231,7 @@
"class BatchCodeTableTest(unittest.TestCase):\n", "class BatchCodeTableTest(unittest.TestCase):\n",
"\n", "\n",
" def test_createBatchCodeTable2(self):\n", " def test_createBatchCodeTable2(self):\n",
" dataFrame = _createDataFrame(\n", " dataFrame = createDataFrameFromDescrs(\n",
" [\n", " [\n",
" {\n", " {\n",
" 'VAERSDATA': self.createDataFrame(\n", " 'VAERSDATA': self.createDataFrame(\n",
@@ -314,14 +321,6 @@
"saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n", "saveBatchCodeTable(\"PFIZER\\BIONTECH\", \"results/pfizer.xlsx\")\n",
"saveBatchCodeTable(\"JANSSEN\", \"results/janssen.xlsx\")" "saveBatchCodeTable(\"JANSSEN\", \"results/janssen.xlsx\")"
] ]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d0f623c1",
"metadata": {},
"outputs": [],
"source": []
} }
], ],
"metadata": { "metadata": {