NiFi: added age limit for cohort script export.

nifi/user-scripts/cogstack_cohort_generate_data.py

@@ -5,6 +5,7 @@
 import os
 import traceback
 import multiprocess
+import random
 
 from multiprocess import Pool, Queue
 from collections import defaultdict, Counter
@@ -47,7 +48,9 @@
 INPUT_PATIENT_RECORD_FILE_NAME_PATTERN = ""
 INPUT_ANNOTATIONS_RECORDS_FILE_NAME_PATTERN = ""
 
-EXPORT_ONLY_PATIENT_RECORDS = "false"
+# if this is enabled, the maximum patient age will be somewhere between 90 and 99 IF there is no DATE OF DEATH available
+# calculated as: current_year - patient_year_of_birth, if > 100, patient_age = rand(90,99)
+ENABLE_PATIENT_AGE_LIMIT = "false"
 
 for arg in sys.argv:
     _arg = arg.split("=", 1)
@@ -81,7 +84,8 @@
         INPUT_PATIENT_RECORD_FILE_NAME_PATTERN = _arg[1]
     if _arg[0] == "input_annotations_records_file_name_pattern":
         INPUT_ANNOTATIONS_RECORDS_FILE_NAME_PATTERN = _arg[1]
-
+    if _arg[0] == "enable_patient_age_limit":
+        ENABLE_PATIENT_AGE_LIMIT = str(_arg[1]).lower()
 
 def _process_patient_records(patient_records: list):
     _ptt2sex, _ptt2eth, _ptt2dob, _ptt2age, _ptt2dod, _doc2ptt = {}, {}, {}, {}, {}, {}
@@ -134,6 +138,9 @@ def _process_patient_records(patient_records: list):
                     patient_age = abs(dod.year - dob.year)
                 else:
                     patient_age = abs(datetime.now().year - dob.year)
+                    if patient_age > 100 and ENABLE_PATIENT_AGE_LIMIT == "true":
+                        dod = datetime.now(tz=timezone.utc)
+                        patient_age = -1
 
                 # convert to ints
                 dod = int(dod.strftime("%Y%m%d%H%M%S")) if dod not in [0, None, "null"] else 0