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making SymptomsByBatchcodesTableFactoryTest pass

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This commit is contained in:
frankknoll
2023-01-19 22:34:22 +01:00
parent a122370c6e
commit df83bcce62
2 changed files with 45 additions and 5 deletions
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32
src/SymptomsByBatchcodesTableFactory.py
View File

@@ -4,5 +4,33 @@ import pandas as pd
class SymptomsByBatchcodesTableFactory:
@staticmethod
def createSymptomsByBatchcodesTable(vaxTable, symptomsTable):
return pd.DataFrame({'A': []})
def createSymptomsByBatchcodesTable(VAERSVAX, VAERSSYMPTOMS):
return pd.merge(
SymptomsByBatchcodesTableFactory._get_VAERSVAX_WITH_VAX_LOTS(VAERSVAX),
SymptomsByBatchcodesTableFactory._getSymptomsTable(VAERSSYMPTOMS),
on = 'VAERS_ID').set_index(['VAX_LOT1', 'VAX_LOT2'])[['SYMPTOMS']]
@staticmethod
def _get_VAERSVAX_WITH_VAX_LOTS(VAERSVAX):
return pd.concat(
[VAERSVAX, SymptomsByBatchcodesTableFactory._getVaxLotsTable(VAERSVAX)],
axis=1).drop_duplicates(subset=['VAX_LOT1', 'VAX_LOT2']).reset_index()
@staticmethod
def _getVaxLotsTable(VAERSVAX):
VAX_LOT_LIST_Table = VAERSVAX.groupby("VAERS_ID").agg(VAX_LOT_LIST = pd.NamedAgg(column = 'VAX_LOT', aggfunc = list))
return pd.DataFrame(
VAX_LOT_LIST_Table['VAX_LOT_LIST'].tolist(),
columns = ['VAX_LOT1', 'VAX_LOT2'],
index = VAX_LOT_LIST_Table.index)
@staticmethod
def _getSymptomsTable(VAERSSYMPTOMS):
return pd.concat(
[
VAERSSYMPTOMS['SYMPTOM1'],
VAERSSYMPTOMS['SYMPTOM2'],
VAERSSYMPTOMS['SYMPTOM3'],
VAERSSYMPTOMS['SYMPTOM4'],
VAERSSYMPTOMS['SYMPTOM5']
]).dropna().drop_duplicates().to_frame(name = "SYMPTOMS").reset_index()

18
src/SymptomsByBatchcodesTableFactoryTest.py
View File

@@ -40,8 +40,20 @@ class SymptomsByBatchcodesTableFactoryTest(unittest.TestCase):
assert_frame_equal(
symptomsByBatchcodesTable,
TestHelper.createDataFrame(
columns = ['Blood pressure orthostatic abnormal', 'COVID-19', 'Coma', 'Computerised tomogram', 'Exposure to SARS-CoV-2', 'Head injury', 'Headache', 'Laboratory test', 'Magnetic resonance imaging', 'SARS-CoV-2 antibody test negative', 'SARS-CoV-2 test positive', 'Unresponsive to stimuli', 'X-ray'],
data = [ [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]],
columns = ['SYMPTOMS'],
data = [ ['Blood pressure orthostatic abnormal'],
['Head injury'],
['SARS-CoV-2 test positive'],
['COVID-19'],
['Headache'],
['Unresponsive to stimuli'],
['Coma'],
['Laboratory test'],
['X-ray'],
['Computerised tomogram'],
['Magnetic resonance imaging'],
['Exposure to SARS-CoV-2'],
['SARS-CoV-2 antibody test negative']],
index = pd.MultiIndex.from_tuples(
names = ['VAX_LOT1', 'VAX_LOT2'],
tuples = [['1808982', 'EW0175']])))
tuples = [['1808982', 'EW0175']] * 13)))