refactoring
This commit is contained in:
frankknoll
@@ -128,7 +128,9 @@
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"class BatchCodeTableFactory:\n",
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" \n",
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" @staticmethod\n",
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" def createBatchCodeTable(df : pd.DataFrame):\n",
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" # FK-TODO: make DataFrame parameter an instance variable\n",
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" def createBatchCodeTable(df : pd.DataFrame, manufacturer, dose):\n",
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" df = DataFrameFilter(df).filterBy(manufacturer = manufacturer, dose = dose)\n",
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" return BatchCodeTableFactory._asDataFrame(\n",
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" {\n",
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" 'ADRs': BatchCodeTableFactory._getADRs(df),\n",
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@@ -139,7 +141,9 @@
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"\n",
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" # create table from https://www.howbadismybatch.com/combined.html\n",
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" @staticmethod\n",
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" def createSevereEffectsBatchCodeTable(df : pd.DataFrame):\n",
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" # FK-TODO: make DataFrame parameter an instance variable\n",
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" def createSevereEffectsBatchCodeTable(df : pd.DataFrame, dose):\n",
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" df = DataFrameFilter(df).filterForSevereEffects(dose = '1')\n",
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" return BatchCodeTableFactory._addCompanyColumn(\n",
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" BatchCodeTableFactory._asDataFrame(\n",
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" {\n",
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@@ -404,7 +408,48 @@
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"source": [
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"from pandas.testing import assert_frame_equal\n",
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"\n",
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"class BatchCodeTableTest(unittest.TestCase):\n",
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"class BatchCodeTableFactoryTest(unittest.TestCase):\n",
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"\n",
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" def test_createSevereEffectsBatchCodeTable(self):\n",
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" # Given\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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" [\n",
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" {\n",
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" 'VAERSDATA': self.createDataFrame(\n",
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" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
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" data = [ ['Y', 'Y', np.NaN, 'Y', 'Y'],\n",
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" [np.NaN, np.NaN, 'Y', np.NaN, 'Y']],\n",
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" index = [\n",
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" \"0916600\",\n",
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" \"0916601\"]),\n",
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" 'VAERSVAX': self.createDataFrame(\n",
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" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
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" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
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" ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
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" index = [\n",
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" \"0916600\",\n",
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" \"0916601\"],\n",
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" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
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" }\n",
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" ]\n",
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" )\n",
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" \n",
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" # When\n",
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" batchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, '1')\n",
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"\n",
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" # Then\n",
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" batchCodeTableExpected = pd.DataFrame(\n",
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" data = {\n",
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" 'ADRs': [1, 1],\n",
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" 'DEATHS': [1, 0],\n",
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" 'DISABILITIES': [0, 1],\n",
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" 'LIFE THREATENING ILLNESSES': [1, 0],\n",
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" 'HOSPITALISATIONS': [1, 0],\n",
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" 'EMERGENCY ROOM OR DOCTOR VISITS': [1, 1],\n",
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" 'COMPANY': ['MODERNA', 'PFIZER\\BIONTECH']\n",
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" },\n",
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" index = pd.Index(['037K20A', '025L20A'], name='VAX_LOT'))\n",
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" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n",
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"\n",
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" def test_createBatchCodeTable2(self):\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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@@ -444,20 +489,16 @@
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" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
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" }\n",
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" ])\n",
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" dataFrame = DataFrameFilter(dataFrame).filterBy(manufacturer = \"MODERNA\", dose = '1')\n",
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" self._test_createBatchCodeTable(dataFrame);\n",
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" self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1');\n",
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"\n",
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" def test_createBatchCodeTable(self):\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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" VaersDescrReader(\"test/VAERS\").readAllVaersDescrs())\n",
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" self._test_createBatchCodeTable(\n",
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" DataFrameFilter(dataFrame).filterBy(\n",
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" manufacturer = \"MODERNA\",\n",
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" dose = '1'))\n",
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" self._test_createBatchCodeTable(dataFrame, \"MODERNA\", '1')\n",
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"\n",
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" def _test_createBatchCodeTable(self, dataFrame):\n",
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" def _test_createBatchCodeTable(self, dataFrame, manufacturer, dose):\n",
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" # When\n",
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" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame)\n",
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" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer, dose)\n",
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"\n",
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" # Then\n",
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" batchCodeTableExpected = pd.DataFrame(\n",
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@@ -474,63 +515,6 @@
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" return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ded70c87",
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"metadata": {},
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"outputs": [],
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"source": [
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"from pandas.testing import assert_frame_equal\n",
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"\n",
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"class SevereEffectsBatchCodeTableTest(unittest.TestCase):\n",
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"\n",
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" def test_createSevereEffectsBatchCodeTable(self):\n",
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" # Given\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
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" [\n",
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" {\n",
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" 'VAERSDATA': self.createDataFrame(\n",
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" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
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" data = [ ['Y', 'Y', np.NaN, 'Y', 'Y'],\n",
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" [np.NaN, np.NaN, 'Y', np.NaN, 'Y']],\n",
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" index = [\n",
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" \"0916600\",\n",
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" \"0916601\"]),\n",
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" 'VAERSVAX': self.createDataFrame(\n",
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" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
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" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
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" ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
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" index = [\n",
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" \"0916600\",\n",
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" \"0916601\"],\n",
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" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
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" }\n",
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" ]\n",
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" )\n",
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" dataFrame = DataFrameFilter(dataFrame).filterForSevereEffects(dose = '1')\n",
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"\n",
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" # When\n",
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" batchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame)\n",
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"\n",
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" # Then\n",
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" batchCodeTableExpected = pd.DataFrame(\n",
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" data = {\n",
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" 'ADRs': [1, 1],\n",
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" 'DEATHS': [1, 0],\n",
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" 'DISABILITIES': [0, 1],\n",
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" 'LIFE THREATENING ILLNESSES': [1, 0],\n",
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" 'HOSPITALISATIONS': [1, 0],\n",
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" 'EMERGENCY ROOM OR DOCTOR VISITS': [1, 1],\n",
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" 'COMPANY': ['MODERNA', 'PFIZER\\BIONTECH']\n",
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" },\n",
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" index = pd.Index(['037K20A', '025L20A'], name='VAX_LOT'))\n",
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" assert_frame_equal(batchCodeTable, batchCodeTableExpected, check_dtype = False)\n",
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"\n",
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" def createDataFrame(self, index, columns, data, dtypes = {}):\n",
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" return pd.DataFrame(index = index, columns = columns, data = data).astype(dtypes)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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@@ -551,8 +535,7 @@
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"def saveBatchCodeTable(manufacturer, excelFile):\n",
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" vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" dataFrameFilter = DataFrameFilter(dataFrame)\n",
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" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrameFilter.filterBy(manufacturer = manufacturer, dose = '1'))\n",
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" batchCodeTable = BatchCodeTableFactory.createBatchCodeTable(dataFrame, manufacturer = manufacturer, dose = '1')\n",
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" display(manufacturer, batchCodeTable)\n",
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" batchCodeTable.to_excel(excelFile)"
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]
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@@ -579,8 +562,7 @@
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"def saveSevereEffectsBatchCodeTable(excelFile):\n",
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" vaersDescrs = VaersDescrReader(\"VAERS\").readAllVaersDescrs()\n",
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" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(vaersDescrs)\n",
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" dataFrameFilter = DataFrameFilter(dataFrame)\n",
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" severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrameFilter.filterForSevereEffects(dose = '1'))\n",
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" severeEffectsBatchCodeTable = BatchCodeTableFactory.createSevereEffectsBatchCodeTable(dataFrame, dose = '1')\n",
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" display('severeEffectsBatchCodeTable', severeEffectsBatchCodeTable)\n",
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" severeEffectsBatchCodeTable.to_excel(excelFile)"
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]
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