removing unused code
This commit is contained in:
frankknoll
@@ -144,29 +144,8 @@
|
|||||||
" def filterByCovid19(self, dataFrame):\n",
|
" def filterByCovid19(self, dataFrame):\n",
|
||||||
" return dataFrame[self._isCovid19(dataFrame)]\n",
|
" return dataFrame[self._isCovid19(dataFrame)]\n",
|
||||||
"\n",
|
"\n",
|
||||||
" def filterByFlu(self, dataFrame):\n",
|
|
||||||
" return dataFrame[self._isFlu(dataFrame)]\n",
|
|
||||||
"\n",
|
|
||||||
" def filterByCountry(self, dataFrame, country, countryColumnName):\n",
|
|
||||||
" return dataFrame[dataFrame[countryColumnName] == country]\n",
|
|
||||||
"\n",
|
|
||||||
" def filterBy(self, dataFrame, manufacturer = None, dose = None):\n",
|
|
||||||
" if manufacturer is None and dose is None:\n",
|
|
||||||
" return dataFrame\n",
|
|
||||||
" \n",
|
|
||||||
" return dataFrame[self._isManufacturer(dataFrame, manufacturer) & self._isDose(dataFrame, dose)]\n",
|
|
||||||
"\n",
|
|
||||||
" def _isCovid19(self, dataFrame):\n",
|
" def _isCovid19(self, dataFrame):\n",
|
||||||
" return dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n",
|
" return dataFrame[\"VAX_TYPE\"] == \"COVID19\"\n"
|
||||||
"\n",
|
|
||||||
" def _isFlu(self, dataFrame):\n",
|
|
||||||
" return dataFrame[\"VAX_TYPE\"].str.startswith(\"FLU\")\n",
|
|
||||||
"\n",
|
|
||||||
" def _isManufacturer(self, dataFrame, manufacturer):\n",
|
|
||||||
" return dataFrame[\"VAX_MANU\"] == manufacturer if manufacturer is not None else True\n",
|
|
||||||
"\n",
|
|
||||||
" def _isDose(self, dataFrame, dose):\n",
|
|
||||||
" return dataFrame[\"VAX_DOSE_SERIES\"].str.contains(dose) if dose is not None else True\n"
|
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
{
|
{
|
||||||
@@ -516,95 +495,7 @@
|
|||||||
"\n",
|
"\n",
|
||||||
"class DataFrameFilterTest(unittest.TestCase):\n",
|
"class DataFrameFilterTest(unittest.TestCase):\n",
|
||||||
"\n",
|
"\n",
|
||||||
" def test_filterByFlu(self):\n",
|
" def test_filterByCovid19(self):\n",
|
||||||
" # Given\n",
|
|
||||||
" dataFrame = TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ [0, 0, 0, 'FLU(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLU3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLU4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUA3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUA4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUC3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUC4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUN(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUN3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUN4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUR3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUR4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUX', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUX(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 1, 'COVID19', 'MODERNA', '025L20A', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"801410\",\n",
|
|
||||||
" \"801411\",\n",
|
|
||||||
" \"801412\",\n",
|
|
||||||
" \"801413\",\n",
|
|
||||||
" \"801414\",\n",
|
|
||||||
" \"801415\",\n",
|
|
||||||
" \"801416\",\n",
|
|
||||||
" \"801417\",\n",
|
|
||||||
" \"801418\",\n",
|
|
||||||
" \"801419\",\n",
|
|
||||||
" \"801420\",\n",
|
|
||||||
" \"801421\",\n",
|
|
||||||
" \"801422\",\n",
|
|
||||||
" \"801423\",\n",
|
|
||||||
" \"801424\"])\n",
|
|
||||||
" dataFrameFilter = DataFrameFilter()\n",
|
|
||||||
" \n",
|
|
||||||
" # When\n",
|
|
||||||
" dataFrameActual = dataFrameFilter.filterByFlu(dataFrame)\n",
|
|
||||||
" \n",
|
|
||||||
" # Then\n",
|
|
||||||
" dataFrameExpected = TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ [0, 0, 0, 'FLU(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLU3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLU4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUA3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUA4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUC3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUC4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUN(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUN3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUN4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUR3', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUR4', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUX', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1'],\n",
|
|
||||||
" [0, 0, 0, 'FLUX(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"801410\",\n",
|
|
||||||
" \"801411\",\n",
|
|
||||||
" \"801412\",\n",
|
|
||||||
" \"801413\",\n",
|
|
||||||
" \"801414\",\n",
|
|
||||||
" \"801415\",\n",
|
|
||||||
" \"801416\",\n",
|
|
||||||
" \"801417\",\n",
|
|
||||||
" \"801418\",\n",
|
|
||||||
" \"801419\",\n",
|
|
||||||
" \"801420\",\n",
|
|
||||||
" \"801421\",\n",
|
|
||||||
" \"801422\",\n",
|
|
||||||
" \"801423\"])\n",
|
|
||||||
" assert_frame_equal(dataFrameActual, dataFrameExpected, check_dtype = False)\n",
|
|
||||||
"\n",
|
|
||||||
" def test_filterByNothing(self):\n",
|
|
||||||
" # Given\n",
|
|
||||||
" dataFrame = TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ [0, 0, 0, 'FLU(H1N1)', 'GLAXOSMITHKLINE BIOLOGICALS', '5R3J5', '1']],\n",
|
|
||||||
" index = [\"801410\"])\n",
|
|
||||||
" dataFrameFilter = DataFrameFilter()\n",
|
|
||||||
" \n",
|
|
||||||
" # When\n",
|
|
||||||
" dataFrameActual = dataFrameFilter.filterBy(dataFrame, manufacturer = None, dose = None)\n",
|
|
||||||
" \n",
|
|
||||||
" # Then\n",
|
|
||||||
" assert_frame_equal(dataFrameActual, dataFrame, check_dtype = True)\n",
|
|
||||||
"\n",
|
|
||||||
" def test_filterByCovid19_filterBy(self):\n",
|
|
||||||
" # Given\n",
|
" # Given\n",
|
||||||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
||||||
" [\n",
|
" [\n",
|
||||||
@@ -626,14 +517,14 @@
|
|||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||||||
" },\n",
|
" },\n",
|
||||||
" {\n",
|
" {\n",
|
||||||
" 'VAERSDATA': TestHelper.createDataFrame(\n",
|
" 'VAERSDATA': TestHelper.createDataFrame(\n",
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
|
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
|
||||||
" data = [ [0, 0, 0],\n",
|
" data = [ [0, 0, 0],\n",
|
||||||
" [0, 0, 1]],\n",
|
" [0, 0, 1]],\n",
|
||||||
" index = [\n",
|
" index = [\n",
|
||||||
" \"1996873\",\n",
|
" \"1996873\",\n",
|
||||||
" \"1996874\"]),\n",
|
" \"1996874\"]),\n",
|
||||||
" 'VAERSVAX': TestHelper.createDataFrame(\n",
|
" 'VAERSVAX': TestHelper.createDataFrame(\n",
|
||||||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
||||||
" data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n",
|
" data = [ ['HPV9', 'MERCK & CO. INC.', 'R017624', 'UNK'],\n",
|
||||||
" ['COVID19', 'MODERNA', '025L20A', '1']],\n",
|
" ['COVID19', 'MODERNA', '025L20A', '1']],\n",
|
||||||
@@ -647,7 +538,6 @@
|
|||||||
" \n",
|
" \n",
|
||||||
" # When\n",
|
" # When\n",
|
||||||
" dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n",
|
" dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n",
|
||||||
" dataFrame = dataFrameFilter.filterBy(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
|
|
||||||
" \n",
|
" \n",
|
||||||
" # Then\n",
|
" # Then\n",
|
||||||
" dataFrameExpected = TestHelper.createDataFrame(\n",
|
" dataFrameExpected = TestHelper.createDataFrame(\n",
|
||||||
@@ -660,115 +550,6 @@
|
|||||||
" \"0916601\",\n",
|
" \"0916601\",\n",
|
||||||
" \"1996874\"],\n",
|
" \"1996874\"],\n",
|
||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
||||||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
|
||||||
"\n",
|
|
||||||
" def test_filterByDose(self):\n",
|
|
||||||
" # Given\n",
|
|
||||||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
|
||||||
" [\n",
|
|
||||||
" {\n",
|
|
||||||
" 'VAERSDATA': TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT'],\n",
|
|
||||||
" data = [ [1, 1, 0, 1, 1],\n",
|
|
||||||
" [0, 0, 1, 0, 1]],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"0916600\",\n",
|
|
||||||
" \"0916601\"]),\n",
|
|
||||||
" 'VAERSVAX': TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ ['COVID19', 'MODERNA', '037K20A', '1'],\n",
|
|
||||||
" ['COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"0916600\",\n",
|
|
||||||
" \"0916601\"],\n",
|
|
||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
|
||||||
" }\n",
|
|
||||||
" ])\n",
|
|
||||||
" dataFrameFilter = DataFrameFilter()\n",
|
|
||||||
" dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n",
|
|
||||||
"\n",
|
|
||||||
" # When\n",
|
|
||||||
" dataFrame = dataFrameFilter.filterBy(dataFrame, dose = '1')\n",
|
|
||||||
" \n",
|
|
||||||
" # Then\n",
|
|
||||||
" dataFrameExpected = TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'HOSPITAL', 'ER_VISIT', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ [1, 1, 0, 1, 1, 'COVID19', 'MODERNA', '037K20A', '1'],\n",
|
|
||||||
" [0, 0, 1, 0, 1, 'COVID19', 'PFIZER\\BIONTECH', '025L20A', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"0916600\",\n",
|
|
||||||
" \"0916601\"],\n",
|
|
||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
|
||||||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
|
||||||
"\n",
|
|
||||||
" def test_filterByFirstDose(self):\n",
|
|
||||||
" # Given\n",
|
|
||||||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
|
||||||
" [\n",
|
|
||||||
" {\n",
|
|
||||||
" 'VAERSDATA': TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
|
|
||||||
" data = [ [1, 0, 0]],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"1048786\"]),\n",
|
|
||||||
" 'VAERSVAX': TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n",
|
|
||||||
" ['COVID19', 'MODERNA', '030L20A', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"1048786\",\n",
|
|
||||||
" \"1048786\"],\n",
|
|
||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
|
||||||
" }\n",
|
|
||||||
" ])\n",
|
|
||||||
" dataFrameFilter = DataFrameFilter()\n",
|
|
||||||
" \n",
|
|
||||||
" # When\n",
|
|
||||||
" dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n",
|
|
||||||
" dataFrame = dataFrameFilter.filterBy(dataFrame, manufacturer = \"MODERNA\", dose = '1')\n",
|
|
||||||
" \n",
|
|
||||||
" # Then\n",
|
|
||||||
" dataFrameExpected = TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ [1, 0, 0, 'COVID19', 'MODERNA', '030L20A', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"1048786\"],\n",
|
|
||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
|
||||||
" assert_frame_equal(dataFrame, dataFrameExpected, check_dtype = False)\n",
|
|
||||||
"\n",
|
|
||||||
" def test_filterBySecondDose(self):\n",
|
|
||||||
" # Given\n",
|
|
||||||
" dataFrame = VaersDescr2DataFrameConverter.createDataFrameFromDescrs(\n",
|
|
||||||
" [\n",
|
|
||||||
" {\n",
|
|
||||||
" 'VAERSDATA': TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE'],\n",
|
|
||||||
" data = [ [1, 0, 0]],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"1048786\"]),\n",
|
|
||||||
" 'VAERSVAX': TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ ['COVID19', 'MODERNA', '016M20A', '2'],\n",
|
|
||||||
" ['COVID19', 'MODERNA', '030L20A', '1']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"1048786\",\n",
|
|
||||||
" \"1048786\"],\n",
|
|
||||||
" dtypes = {'VAX_DOSE_SERIES': \"string\"})\n",
|
|
||||||
" }\n",
|
|
||||||
" ])\n",
|
|
||||||
" dataFrameFilter = DataFrameFilter()\n",
|
|
||||||
"\n",
|
|
||||||
" # When\n",
|
|
||||||
" dataFrame = dataFrameFilter.filterByCovid19(dataFrame)\n",
|
|
||||||
" dataFrame = dataFrameFilter.filterBy(dataFrame, manufacturer = \"MODERNA\", dose = '2')\n",
|
|
||||||
" \n",
|
|
||||||
" # Then\n",
|
|
||||||
" dataFrameExpected = TestHelper.createDataFrame(\n",
|
|
||||||
" columns = ['DIED', 'L_THREAT', 'DISABLE', 'VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],\n",
|
|
||||||
" data = [ [1, 0, 0, 'COVID19', 'MODERNA', '016M20A', '2']],\n",
|
|
||||||
" index = [\n",
|
|
||||||
" \"1048786\"],\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"
|
||||||
]
|
]
|
||||||
},
|
},
|
||||||
|
|||||||
Reference in New Issue
Block a user