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BICF
KCE
kce_etl
Commits
b9b0587e
Commit
b9b0587e
authored
Apr 20, 2020
by
Venkat Malladi
Browse files
Update patients.
parent
d47e352e
Changes
2
Hide whitespace changes
Inline
Side-by-side
scripts/transform_patients.py
View file @
b9b0587e
...
...
@@ -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
)
...
...
tests/test_transform_patients.py
View file @
b9b0587e
...
...
@@ -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,D
ate
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,D
EATH_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_d
iagnosis
():
def
demographic_d
eath
():
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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