Fix medications.

scripts/transform_medications.py

@@ -47,8 +47,8 @@ def get_args():
     return args
 
 
-def filter_supplemental(epic, sup, meds_map):
-    '''Filter by supplemental med name'''
+def filter_supportive(epic, sup, meds_map):
+    '''Filter by supportive med name'''
 
     # Filter for columns
     sup_list = list(sup['ID'])
@@ -184,7 +184,6 @@ def calculate_regime(meds):
     onco_meds_reformated.loc[onco_meds_reformated.End_date > datetime.datetime(2020, 3, 1), 'Duration'] = None
 
     # If End_date is null
-    #onco_meds_reformated.loc[onco_meds_reformated.End_date.isnull(), 'Duration'] = None
     onco_meds_reformated.loc[onco_meds_reformated.End_date.isnull(), 'End_date'] = datetime.datetime(2020, 3, 1)
     onco_meds_reformated['Duration'] = (onco_meds_reformated['End_date'] - onco_meds_reformated['Start_date']).dt.days
 
@@ -205,9 +204,10 @@ def calculate_shift(meds, date_shift):
 
     # Calculate Date Shift
     merged['Start_date'] = merged['Start_date'] + merged['Shift']
-
+    merged['Start_date'] = merged['Start_date'].dt.date
     if 'End_date' in merged.columns:
         merged['End_date'] = merged['End_date'] + merged['Shift']
+        merged['End_date'] = merged['End_date'].dt.date
 
     # Drop Shift column
     merged.drop(['Shift'], axis=1, inplace=True)
@@ -239,7 +239,7 @@ def main():
     date_shift = pd.read_csv(date)
 
     # Filter for supplemental meds
-    supp_meds, onco_meds, missing_meds = filter_supplemental(epic_df, supmedsmap_df, medsmap_df)
+    supp_meds, onco_meds, missing_meds = filter_supportive(epic_df, supmedsmap_df, medsmap_df)
 
     # Find Supplemental Meds Frequency
     supp_meds_regime, filtered_supp_meds = filter_supp(supp_meds)
@@ -254,9 +254,11 @@ def main():
 
     # Write out meds tables
     supp_meds_regime_shifted_df.to_csv(suppmeds_table, index=False)
-    onco_meds_regime.to_csv(meds_table, index=False)
-    missing_meds.to_csv(unmapped_table, index=False)
-    filtered_supp_meds.to_csv(not_given_suppmeds_table, index=False)
+    onco_meds_shifted_df.to_csv(meds_table, index=False)
+    if missing_meds.shape[0] > 1:
+        missing_meds.to_csv(unmapped_table, index=False)
+    if filtered_supp_meds.shape[0] > 1:
+        filtered_supp_meds.to_csv(not_given_suppmeds_table, index=False)
 
 
 if __name__ == '__main__':