Fix cancer medication mapping

scripts/transform_medications.py

@@ -179,12 +179,14 @@ def calculate_regime(meds):
     onco_meds_reformated.loc[onco_meds_reformated.Duration == 0, 'End_date'] = None
     onco_meds_reformated.loc[onco_meds_reformated.Duration == 0, 'Duration'] = None
 
-    # If End Date > thatn current pull reset to null
-    onco_meds_reformated.loc[onco_meds_reformated.End_date > datetime.datetime(2019, 1, 1), 'End_date'] = None
-    onco_meds_reformated.loc[onco_meds_reformated.End_date > datetime.datetime(2019, 1, 1), 'Duration'] = None
+    # If End Date > that current pull reset to null
+    onco_meds_reformated.loc[onco_meds_reformated.End_date > datetime.datetime(2020, 3, 1), 'End_date'] = None
+    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(), '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
 
     onco_meds_reformated = onco_meds_reformated.reset_index(drop=True)
 
@@ -252,7 +254,7 @@ def main():
 
     # Write out meds tables
     supp_meds_regime_shifted_df.to_csv(suppmeds_table, index=False)
-    onco_meds_shifted_df.to_csv(meds_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)
 

standards/cancer_meds_map.csv

@@ -119,6 +119,7 @@ Nivolumab,MED:853030
 Nivolumab,MED:853140
 Nivolumab,MED:853167
 Nivolumab,MED:853250
+Nivolumab,MED:853316
 NKTR-214,MED:853361
 NKTR-262,MED:853372
 Pazopanib,MED:237450