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refactoring

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This commit is contained in:
frankknoll
2023-01-23 08:07:23 +01:00
parent 28e71af7af
commit b6eb929a7b
2 changed files with 18 additions and 18 deletions
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14
src/SymptomsByBatchcodesTableFactory.py → src/SymptomByBatchcodeTableFactory.py
View File

@@ -1,20 +1,20 @@
import pandas as pd import pandas as pd
import numpy as np import numpy as np
class SymptomsByBatchcodesTableFactory: class SymptomByBatchcodeTableFactory:
@staticmethod @staticmethod
def createSymptomsByBatchcodesTable(VAERSVAX, VAERSSYMPTOMS): def createSymptomByBatchcodeTable(VAERSVAX, VAERSSYMPTOMS):
index_columns = SymptomsByBatchcodesTableFactory._getIndexColumns(VAERSVAX) index_columns = SymptomByBatchcodeTableFactory._getIndexColumns(VAERSVAX)
symptomColumn = 'SYMPTOM' symptomColumn = 'SYMPTOM'
return pd.merge( return pd.merge(
SymptomsByBatchcodesTableFactory._get_VAERSVAX_WITH_VAX_LOTS(VAERSVAX, index_columns), SymptomByBatchcodeTableFactory._get_VAERSVAX_WITH_VAX_LOTS(VAERSVAX, index_columns),
SymptomsByBatchcodesTableFactory._getSymptomsTable(VAERSSYMPTOMS, symptomColumn), SymptomByBatchcodeTableFactory._getSymptomsTable(VAERSSYMPTOMS, symptomColumn),
on = 'VAERS_ID').set_index(index_columns)[[symptomColumn]] on = 'VAERS_ID').set_index(index_columns)[[symptomColumn]]
@staticmethod @staticmethod
def _getIndexColumns(VAERSVAX): def _getIndexColumns(VAERSVAX):
return [f"VAX_LOT{num}" for num in range(1, SymptomsByBatchcodesTableFactory._getMaxNumShots(VAERSVAX) + 1)] return [f"VAX_LOT{num}" for num in range(1, SymptomByBatchcodeTableFactory._getMaxNumShots(VAERSVAX) + 1)]
@staticmethod @staticmethod
def _getMaxNumShots(VAERSVAX): def _getMaxNumShots(VAERSVAX):
@@ -23,7 +23,7 @@ class SymptomsByBatchcodesTableFactory:
@staticmethod @staticmethod
def _get_VAERSVAX_WITH_VAX_LOTS(VAERSVAX, index_columns): def _get_VAERSVAX_WITH_VAX_LOTS(VAERSVAX, index_columns):
return pd.concat( return pd.concat(
[VAERSVAX, SymptomsByBatchcodesTableFactory._getVaxLotsTable(VAERSVAX, index_columns)], [VAERSVAX, SymptomByBatchcodeTableFactory._getVaxLotsTable(VAERSVAX, index_columns)],
axis='columns').reset_index().drop_duplicates(subset = ['VAERS_ID'] + index_columns) axis='columns').reset_index().drop_duplicates(subset = ['VAERS_ID'] + index_columns)
@staticmethod @staticmethod

22
src/SymptomsByBatchcodesTableFactoryTest.py → src/SymptomByBatchcodeTableFactoryTest.py
View File

@@ -1,14 +1,14 @@
import unittest import unittest
from pandas.testing import assert_frame_equal from pandas.testing import assert_frame_equal
from TestHelper import TestHelper from TestHelper import TestHelper
from SymptomsByBatchcodesTableFactory import SymptomsByBatchcodesTableFactory from SymptomByBatchcodeTableFactory import SymptomByBatchcodeTableFactory
import pandas as pd import pandas as pd
import numpy as np import numpy as np
# FIXME: brauchen Normalisierung analog zu DataFrameNormalizer.removeUnknownBatchCodes(dataFrame) und DataFrameNormalizer.convertVAX_LOTColumnToUpperCase(dataFrame) # FIXME: brauchen Normalisierung analog zu DataFrameNormalizer.removeUnknownBatchCodes(dataFrame) und DataFrameNormalizer.convertVAX_LOTColumnToUpperCase(dataFrame)
class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase): class SymptomByBatchcodeTableFactoryTest(unittest.TestCase):
def test_createSymptomsByBatchcodesTable(self): def test_createSymptomByBatchcodeTable(self):
# Given # Given
VAERSVAX = TestHelper.createDataFrame( VAERSVAX = TestHelper.createDataFrame(
columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'], columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],
@@ -35,11 +35,11 @@ class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase):
2547730])) 2547730]))
# When # When
symptomsByBatchcodesTable = SymptomsByBatchcodesTableFactory.createSymptomsByBatchcodesTable(VAERSVAX, VAERSSYMPTOMS) symptomByBatchcodeTable = SymptomByBatchcodeTableFactory.createSymptomByBatchcodeTable(VAERSVAX, VAERSSYMPTOMS)
# Then # Then
assert_frame_equal( assert_frame_equal(
symptomsByBatchcodesTable, symptomByBatchcodeTable,
TestHelper.createDataFrame( TestHelper.createDataFrame(
columns = ['SYMPTOM'], columns = ['SYMPTOM'],
data = [ ['Blood pressure orthostatic abnormal'], data = [ ['Blood pressure orthostatic abnormal'],
@@ -59,7 +59,7 @@ class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase):
names = ['VAX_LOT1', 'VAX_LOT2'], names = ['VAX_LOT1', 'VAX_LOT2'],
tuples = [['1808982', 'EW0175']] * 13))) tuples = [['1808982', 'EW0175']] * 13)))
def test_createSymptomsByBatchcodesTable_two_patients_same_symptoms(self): def test_createSymptomByBatchcodeTable_two_patients_same_symptoms(self):
# Given # Given
VAERSVAX = TestHelper.createDataFrame( VAERSVAX = TestHelper.createDataFrame(
columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'], columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],
@@ -84,11 +84,11 @@ class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase):
2547731])) 2547731]))
# When # When
symptomsByBatchcodesTable = SymptomsByBatchcodesTableFactory.createSymptomsByBatchcodesTable(VAERSVAX, VAERSSYMPTOMS) symptomByBatchcodeTable = SymptomByBatchcodeTableFactory.createSymptomByBatchcodeTable(VAERSVAX, VAERSSYMPTOMS)
# Then # Then
assert_frame_equal( assert_frame_equal(
symptomsByBatchcodesTable, symptomByBatchcodeTable,
TestHelper.createDataFrame( TestHelper.createDataFrame(
columns = ['SYMPTOM'], columns = ['SYMPTOM'],
data = [ ['Blood pressure orthostatic abnormal'], data = [ ['Blood pressure orthostatic abnormal'],
@@ -99,7 +99,7 @@ class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase):
'EW0175'])), 'EW0175'])),
check_dtype = False) check_dtype = False)
def test_createSymptomsByBatchcodesTable_two_patients_distinct_symptoms(self): def test_createSymptomByBatchcodeTable_two_patients_distinct_symptoms(self):
# Given # Given
VAERSVAX = TestHelper.createDataFrame( VAERSVAX = TestHelper.createDataFrame(
columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'], columns = ['VAX_TYPE', 'VAX_MANU', 'VAX_LOT', 'VAX_DOSE_SERIES'],
@@ -134,11 +134,11 @@ class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase):
2547744])) 2547744]))
# When # When
symptomsByBatchcodesTable = SymptomsByBatchcodesTableFactory.createSymptomsByBatchcodesTable(VAERSVAX, VAERSSYMPTOMS) symptomByBatchcodeTable = SymptomByBatchcodeTableFactory.createSymptomByBatchcodeTable(VAERSVAX, VAERSSYMPTOMS)
# Then # Then
assert_frame_equal( assert_frame_equal(
symptomsByBatchcodesTable, symptomByBatchcodeTable,
TestHelper.createDataFrame( TestHelper.createDataFrame(
columns = ['SYMPTOM'], columns = ['SYMPTOM'],
data = [ ['Blood pressure orthostatic abnormal'], data = [ ['Blood pressure orthostatic abnormal'],