Make lower case.

scripts/transform_medications.py

@@ -79,7 +79,7 @@ def filter_supp(supp_meds):
 
     #Filter columns
     supp_meds_reformated = meds_taken[['MRN', 'Meds', 'START_DATE']]
-    supp_meds_reformated.columns = ['mrn', 'name', 'Start_date']
+    supp_meds_reformated.columns = ['mrn', 'name', 'start_date']
 
     return supp_meds_reformated, meds_non_taken
 
@@ -170,22 +170,22 @@ def calculate_regime(meds):
     # Format Oncological Meds
     meds_filtered_uniq = meds_transformed.groupby(['mrn', 'name'], as_index=False).agg({'date' : [np.min, np.max], 'start' : [np.min], 'end' : [np.max]   })
     meds_filtered_uniq.columns = ['mrn', 'name','date_start', 'date_end', 'start', 'end']
-    meds_filtered_uniq['Start_date'] = meds_filtered_uniq[['date_start', 'date_end', 'start', 'end']].min(axis=1)
-    meds_filtered_uniq['End_date'] = meds_filtered_uniq[['date_start', 'date_end', 'start', 'end']].max(axis=1)
-    meds_filtered_uniq['Duration'] = (meds_filtered_uniq['End_date'] - meds_filtered_uniq['Start_date']).dt.days
-    onco_meds_reformated = meds_filtered_uniq[['mrn', 'name', 'Start_date', 'End_date', 'Duration']]
+    meds_filtered_uniq['start_date'] = meds_filtered_uniq[['date_start', 'date_end', 'start', 'end']].min(axis=1)
+    meds_filtered_uniq['end_date'] = meds_filtered_uniq[['date_start', 'date_end', 'start', 'end']].max(axis=1)
+    meds_filtered_uniq['Duration'] = (meds_filtered_uniq['end_date'] - meds_filtered_uniq['start_date']).dt.days
+    onco_meds_reformated = meds_filtered_uniq[['mrn', 'name', 'start_date', 'end_date', 'Duration']]
 
     # Reset duration for 0
-    onco_meds_reformated.loc[onco_meds_reformated.Duration == 0, 'End_date'] = None
+    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 > 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
+    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(), '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.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)
 
@@ -197,17 +197,17 @@ def calculate_shift(meds, date_shift):
 
     # Convert to DateTime
     date_shift['Shift'] = pd.to_timedelta(date_shift['Shift'], unit='s')
-    meds['Start_date'] = pd.to_datetime(meds['Start_date'])
+    meds['start_date'] = pd.to_datetime(meds['start_date'])
 
     # Merge data
     merged = meds.merge(date_shift, left_on='mrn', right_on='MRN', how='inner')
 
     # 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
+    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)