Merge pull request #149 from seattleflu/invalid-birth-date

etl redcap-det uw-reopening: Handle invalid birth date

lib/seattleflu/id3c/cli/command/etl/redcap_det_uw_reopening.py

@@ -125,7 +125,7 @@ def redcap_det_uw_reopening(*, db: DatabaseSession, cache: TTLCache, det: dict,
         return None
 
     patient_entry, patient_reference = create_patient(enrollment)
-    birthdate = datetime.strptime(enrollment['core_birthdate'], '%Y-%m-%d')
+    birthdate = parse_birth_date(enrollment)
 
     if not patient_entry:
         LOG.warning("Skipping record with insufficient information to construct patient")
@@ -253,6 +253,17 @@ def redcap_det_uw_reopening(*, db: DatabaseSession, cache: TTLCache, det: dict,
     )
 
 
+def parse_birth_date(record: dict) -> Optional[datetime]:
+    """ Returns a participant's birth date from a given *record* as a datetime
+    object if it can be parsed. Otherwise, emits a warning and returns None. """
+    try:
+        birth_date = datetime.strptime(record['core_birthdate'], '%Y-%m-%d')
+    except ValueError:
+        LOG.warning("Invalid `core_birthdate`.")
+        birth_date = None
+
+    return birth_date
+
 def create_site_reference(record: dict, collection_method: CollectionMethod, event_type: EventType) -> Optional[Dict[str,dict]]:
     """
     Create a Location reference for site of the sample collection encounter based
@@ -1147,8 +1158,13 @@ def create_computed_questionnaire_response(record: dict, patient_reference: dict
     For example, a computed question captures the participant's age
     on the date of the encounter.
     """
-
-    record['age'] = relativedelta(encounter_date, birthdate).years
+    # A birthdate of None will return a falsy relativedelta() object
+    delta = relativedelta(encounter_date, birthdate)
+    if not delta:
+        age = None
+    else:
+        age = delta.years
+    record['age'] = age
 
     integer_questions = [
         'age'