fix(fhir): Fixes FHIR date formatting; includes flattened patient in …

…query results

Merge pull request #5 from hms-dbmi/development

ppmutils/fhir.py

@@ -390,6 +390,11 @@ def _format_date(date_string, date_format):
             to_zone = tz.gettz('America/New_York')
             utc = date.replace(tzinfo=from_zone)
 
+            # If UTC time was 00:00:00, assume a time was missing and return the date as is so
+            # the ET conversion does not change the date.
+            if utc.hour == 0 and utc.minute == 0 and utc.second == 0:
+                return utc.strftime(date_format)
+
             # Convert time zone to assumed ET
             et = utc.astimezone(to_zone)
 
@@ -1091,25 +1096,10 @@ def query_patients(study=None, enrollment=None, active=True, testing=False):
                     'date_registered': date_registered,
                 }
 
-                # Check names
-                try:
-                    patient_dict['firstname'] = patient.name[0].given[0]
-                except Exception:
-                    patient_dict['firstname'] = "---"
-                    logger.warning('No firstname for Patient/{}'.format(patient.id))
-                try:
-                    patient_dict['lastname'] = patient.name[0].family
-                except Exception:
-                    patient_dict['lastname'] = "---"
-                    logger.warning('No lastname for Patient/{}'.format(patient.id))
-
-                # Add twitter handle
-                try:
-                    for telecom in patient.telecom:
-                        if telecom.system == "other" and telecom.value.startswith("https://twitter.com"):
-                            patient_dict['twitter_handle'] = telecom.value
-                except Exception:
-                    pass
+                # Wrap the patient resource in a fake bundle and flatten them
+                flattened_patient = FHIR.flatten_patient({'entry': [{'resource': patient.as_json()}]})
+                if flattened_patient:
+                    patient_dict.update(flattened_patient)
 
                 # Add it
                 patients.append(patient_dict)
@@ -2487,7 +2477,7 @@ def flatten_participant(bundle):
             if enrollment['enrollment'] == PPM.Enrollment.Accepted.value and enrollment.get('start'):
 
                 # Convert time zone to assumed ET
-                participant['enrollment_accepted_date'] = FHIR._format_date(enrollment['start'], '%-m/%-d/%Y')
+                participant['enrollment_accepted_date'] = FHIR._format_date(enrollment['start'], '%m/%d/%Y')
 
             else:
                 participant['enrollment_accepted_date'] = ''
@@ -2624,6 +2614,10 @@ def flatten_questionnaire_response(bundle_dict, questionnaire_id):
             # Add the answer
             response[text] = answer
 
+        # Add the date that the questionnaire was completed
+        authored_date = questionnaire_response.authored.origval
+        formatted_authored_date = FHIR._format_date(authored_date, '%m/%d/%Y')
+
         return response
 
     @staticmethod
@@ -2891,7 +2885,7 @@ def flatten_consent_composition(bundle_json):
                     date_time = signed_consent.dateTime.origval
 
                     # Format it
-                    consent_object["date_signed"] = FHIR._format_date(date_time, '%Y-%m-%d')
+                    consent_object["date_signed"] = FHIR._format_date(date_time, '%m/%d/%Y')
 
                     # Exceptions are for when they refuse part of the consent.
                     if signed_consent.except_fhir:
@@ -3118,7 +3112,7 @@ def flatten_document_reference(resource):
         # Get dates
         reference['timestamp'] = FHIR._get_or(resource, ['indexed'])
         if reference.get('timestamp'):
-            reference['date'] = FHIR._format_date(reference['timestamp'], '%m-%d-%Y')
+            reference['date'] = FHIR._format_date(reference['timestamp'], '%m/%d/%Y')
 
         # Get data provider
         reference['code'] = FHIR._get_or(resource, ['type', 'coding', 0, 'code'])