Update radiation logic to include end date.

scripts/transform_radiation_history.py

@@ -92,7 +92,7 @@ def convert_sites(radiation, sites):
     # Filter for columns
     filter_col = ["MRN", "SITE_SPECIFIC", "SITE_GENERAL",
                 "DOSE_CGY_ACTUAL", "FRACTIONS_ACTUAL",
-                "STARTDATE", "TREATINTENT"]
+                "STARTDATE", "LASTDATE", "TREATINTENT"]
     radiation_filtered = radiation_mapped.loc[:, filter_col]
 
     # Remove commas in
@@ -110,11 +110,12 @@ def convert_treatment(merged):
 
 
 def calculate_shift(radiation, date_shift):
-    '''Shift Date for start date'''
+    '''Shift Date for start and last date'''
 
     # Convert to DateTime
     date_shift['Shift'] = pd.to_timedelta(date_shift['Shift'], unit='s')
     radiation['STARTDATE'] = pd.to_datetime(radiation['STARTDATE'])
+    radiation['LASTDATE'] = pd.to_datetime(radiation['LASTDATE'])
 
     # Merge data
     merged = radiation.merge(date_shift, left_on='MRN', right_on='MRN', how='inner')
@@ -123,6 +124,9 @@ def calculate_shift(radiation, date_shift):
     merged['STARTDATE'] = merged['STARTDATE'] + merged['Shift']
     merged['STARTDATE'] = merged['STARTDATE'].dt.date
 
+    merged['LASTDATE'] = merged['LASTDATE'] + merged['Shift']
+    merged['LASTDATE'] = merged['LASTDATE'].dt.date
+
 
     # Drop Shift column
     merged.drop(['Shift'], axis=1, inplace=True)
@@ -134,7 +138,7 @@ def calculate_shift(radiation, date_shift):
 
     # Rename columns
     radiation_columns = ["mrn", "site_specific", "site_general",
-                   "dose_cgy_actual", "fractions_actual", 'start_date', 'treatment_intention']
+                   "dose_cgy_actual", "fractions_actual", 'start_date', 'end_date', 'treatment_intention']
     merged.columns = radiation_columns
 
     return merged

tests/data/radiation_sitemap.csv

 MRN,SITE_SPECIFIC,SITE_GENERAL,DOSE_CGY_ACTUAL,FRACTIONS_ACTUAL,STARTDATE,TREATINTENT,Sites
 934,Liver,Liver,3000,5,1/5/2013,Curative,Liver
-313,Femur,Bone and bone marrow,2000,1,8/25/2011,Palliative,Bone/Bone marrow/Spine
+313,Femur,Bone,2000,1,8/25/2011,Palliative,Bone/Bone marrow/Spine
 313,Spine,Spine,2000,1,8/25/2011,Palliative,Bone/Bone marrow/Spine
 903,0A:1 L frontal,Brain,1300,1,2/4/2017,Not Available,Brain
 903,0B:2 R Cor Callos,Brain,1300,1,2/4/2017,Not Available,Brain
@@ -10,5 +10,5 @@ MRN,SITE_SPECIFIC,SITE_GENERAL,DOSE_CGY_ACTUAL,FRACTIONS_ACTUAL,STARTDATE,TREATI
 687,prostate gland,Prostate gland,2700,15,6/27/2009,Curative,Other
 687,PTV RUL 40Gy5fx,"Lung, right",4000,5,8/18/2013,Consolidative,Lung
 423,RtAdrenal,"Adrenal gland, right",3600,3,4/29/2015,Consolidative,Adrenal
-88,L shoulder,Bone and bone marrow,3000,10,7/4/2009,Not Available,Bone/Bone marrow/Spine
-88,R Hip,Bone and bone marrow,3000,5,2/20/2010,De-Bulking,Bone/Bone marrow/Spine
+88,L shoulder,Bone,3000,10,7/4/2009,Not Available,Bone/Bone marrow/Spine
+88,R Hip,Bone,3000,5,2/20/2010,De-Bulking,Bone/Bone marrow/Spine

tests/transform/radiation_table.csv

-mrn,site_specific,site_general,dose_cgy_actual,fractions_actual,start_date,treatment_intention
-313,Femur,Bone and bone marrow,2000.0,1.0,1857-06-14,Palliative
-313,Spine,Spine,2000.0,1.0,1857-06-14,Palliative
-423,RtAdrenal,"Adrenal gland, right",3600.0,3.0,1870-05-26,Consolidative
-687,PTV RUL 40Gy5fx,"Lung, right",4000.0,5.0,1855-02-05,Consolidative
-822,Abdomen,Retroperitoneum & peritoneum,2500.0,5.0,1901-01-30,Not Available
-88,L shoulder,Bone and bone marrow,3000.0,10.0,1858-10-22,Not Available
-88,R Hip,Bone and bone marrow,3000.0,5.0,1859-06-10,De-Bulking
-903,0A:1 L frontal,Brain,1300.0,1.0,1824-05-21,Not Available
-903,0B:2 R Cor Callos,Brain,1300.0,1.0,1824-05-21,Not Available
-903,0C:3 R ventral po,Brain,1300.0,1.0,1824-05-21,Not Available
-903,0D:4 R eye,Brain,1300.0,1.0,1824-05-21,Not Available
-934,Liver,Liver,3000.0,5.0,1855-07-13,Curative
+mrn,site_specific,site_general,dose_cgy_actual,fractions_actual,start_date,end_date,treatment_intention
+313,Femur,Bone,2000.0,1.0,1857-06-14,1857-06-14,Palliative
+313,Spine,Spine,2000.0,1.0,1857-06-14,1857-06-14,Palliative
+423,RtAdrenal,"Adrenal gland, right",3600.0,3.0,1870-05-26,1870-05-26,Consolidative
+687,PTV RUL 40Gy5fx,"Lung, right",4000.0,5.0,1855-02-05,1855-02-27,Consolidative
+822,Abdomen,Retroperitoneum & peritoneum,2500.0,5.0,1901-01-30,1901-02-19,Not Available
+88,L shoulder,Bone,3000.0,10.0,1858-10-22,1858-11-15,Not Available
+88,R Hip,Bone,3000.0,5.0,1859-06-10,1859-06-19,De-Bulking
+903,0A:1 L frontal,Brain,1300.0,1.0,1824-05-21,1824-05-21,Not Available
+903,0B:2 R Cor Callos,Brain,1300.0,1.0,1824-05-21,1824-05-21,Not Available
+903,0C:3 R ventral po,Brain,1300.0,1.0,1824-05-21,1824-05-21,Not Available
+903,0D:4 R eye,Brain,1300.0,1.0,1824-05-21,1824-05-21,Not Available
+934,Liver,Liver,3000.0,5.0,1855-07-13,1855-07-28,Curative