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BICF
KCE
kce_etl
Commits
4d4bc761
Commit
4d4bc761
authored
Apr 20, 2020
by
Venkat Malladi
Browse files
Linted coded.
parent
b9b0587e
Changes
1
Hide whitespace changes
Inline
Side-by-side
scripts/transform_patients.py
View file @
4d4bc761
...
...
@@ -40,7 +40,8 @@ def filter_table(demographics, tumor_registry):
'''Filter demographics and tumor_registry columns'''
# Column filters
demo_filter_col
=
[
"MRN"
,
"GENDER"
,
"ETHNICITY"
,
"RACE"
,
"BIRTH_DATE"
,
"DEATH_DATE"
,
"DEATH_SOURCE"
]
demo_filter_col
=
[
"MRN"
,
"GENDER"
,
"ETHNICITY"
,
"RACE"
,
"BIRTH_DATE"
,
"DEATH_DATE"
,
"DEATH_SOURCE"
]
tumor_filter_col
=
[
"Medical Record Number"
,
"Date of Last Contact-Date"
,
"Vital Status"
]
# Filter
...
...
@@ -51,7 +52,8 @@ def filter_table(demographics, tumor_registry):
tumor_dead
=
tumor_filter
[
tumor_filter
[
"Vital Status"
]
==
0
]
# merge
df_merged
=
demo_filter
.
merge
(
tumor_dead
,
left_on
=
'MRN'
,
right_on
=
'Medical Record Number'
,
how
=
'left'
)
df_merged
=
demo_filter
.
merge
(
tumor_dead
,
left_on
=
'MRN'
,
right_on
=
'Medical Record Number'
,
how
=
'left'
)
return
df_merged
...
...
@@ -145,7 +147,8 @@ def main():
shifted_df
=
calculate_shift
(
fix_race
)
# Write out patients table
shifted_filtered
=
shifted_df
[[
"MRN"
,
"GENDER"
,
"ETHNICITY"
,
"RACE"
,
'DEATH_DATE'
,
'DEATH_SOURCE'
]]
shifted_filtered
=
shifted_df
[[
"MRN"
,
"GENDER"
,
"ETHNICITY"
,
"RACE"
,
'DEATH_DATE'
,
'DEATH_SOURCE'
]]
shifted_filtered
.
columns
=
[
'mrn'
,
'gender'
,
'ethnicity'
,
'race'
,
'death_date'
,
'death_source'
]
shifted_filtered
.
to_csv
(
patients
,
index
=
False
)
...
...
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