Commit b9b0587e authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update patients.

parent d47e352e
......@@ -102,12 +102,11 @@ def calculate_shift(merged):
# Update death date if from tumor registry
merged.loc[pd.notna(merged['Vital Status']), 'DEATH_SOURCE'] = 'Tumor Registry'
merged.loc[pd.notna(merged['Vital Status']), 'DEATH_DATE'] = 'Date of Last Contact-Date'
merged.loc[pd.notna(merged['Vital Status']), 'DEATH_DATE'] = merged['Date of Last Contact-Date']
# Calculate date Shift for death date
merged['DEATH_DATE'] = merged['DEATH_DATE'] + merged['Shift']
# Shift to total seconds
time_delta_series = merged['Shift']
merged['Shift'] = time_delta_series.apply(get_seconds)
......
......@@ -11,9 +11,9 @@ DEMOGRAPHIC_STRING = """MRN,PAT_ID,PAT_LAST_NAME,PAT_FIRST_NAME,GENDER,BIRTH_DAT
"""
DEMO_MERGED_STRING = """MRN,GENDER,ETHNICITY,RACE,BIRTH_DATE,Date
934,FEMALE,AmIndAN,@,27-JUN-1957,11/27/2017
822,FEMALE,White,@,29-JUL-1913,03/10/2015
DEMO_MERGED_STRING = """MRN,GENDER,ETHNICITY,RACE,BIRTH_DATE,DEATH_DATE,DEATH_SOURCE,Date of Last Contact-Date,Vital Status
934,FEMALE,AmIndAN,@,27-JUN-1957,11/27/2017,EPIC,,
822,FEMALE,White,@,29-JUL-1913,,,03/10/2015,0
"""
......@@ -25,7 +25,7 @@ def demographic():
@pytest.fixture
def demographic_diagnosis():
def demographic_death():
merged_file = StringIO(DEMO_MERGED_STRING)
merged_df = pd.read_csv(merged_file)
return merged_df
......@@ -81,14 +81,16 @@ def test_check_race_unknown(demographic_2):
@pytest.mark.unit
def test_check_shift(demographic_diagnosis):
check_shift = transform_patients.calculate_shift(demographic_diagnosis)
assert check_shift.loc[0,'Age'] == 60
def test_check_shift(demographic_death):
check_shift = transform_patients.calculate_shift(demographic_death)
check_shift['DEATH_DATE'] = check_shift['DEATH_DATE'].astype(str)
assert check_shift.loc[0,'DEATH_DATE'] == '1860-06-03'
assert check_shift.loc[0,'Shift'] == -4969728000.0
@pytest.mark.unit
def test_check_shift_90_over(demographic_diagnosis):
check_shift_90_over = transform_patients.calculate_shift(demographic_diagnosis)
assert check_shift_90_over.loc[1,'Age'] == '90 or above'
assert check_shift_90_over.loc[1,'Shift'] == -3583958400.0
def test_check_shift_tumor_registry(demographic_death):
check_shift_tumor_registry = transform_patients.calculate_shift(demographic_death)
check_shift_tumor_registry['DEATH_DATE'] = check_shift_tumor_registry['DEATH_DATE'].astype(str)
assert check_shift_tumor_registry.loc[1,'DEATH_DATE'] == '1901-08-14'
assert check_shift_tumor_registry.loc[1,'Shift'] == -3583958400.0
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