Linted coded.

scripts/transform_patients.py

@@ -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)