fix(fhir): Fixed issues caused by fhirclient v4.2.0

hms-dbmi · Jul 27, 2024 · 12ced4e · 12ced4e
1 parent cc8f36a
commit 12ced4e
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Showing 3 changed files with 30 additions and 26 deletions.
diff --git a/ppmutils/fhir.py b/ppmutils/fhir.py
@@ -25,6 +25,8 @@
 from fhirclient.models.domainresource import DomainResource
 from fhirclient.models.fhirdate import FHIRDate
 from fhirclient.models.period import Period
+from fhirclient.models.fhirinstant import FHIRInstant
+from fhirclient.models.fhirdatetime import FHIRDateTime
 from fhirclient.models.patient import Patient
 from fhirclient.models.flag import Flag
 from fhirclient.models.bundle import Bundle, BundleEntry, BundleEntryRequest
@@ -4547,7 +4549,7 @@ def update_patient_enrollment(patient: Union[Patient, dict, str], status: str, s
                         flag.period.end = None
 
                     else:
-                        now = FHIRDate(datetime.now(timezone.utc).isoformat())
+                        now = FHIRDateTime(datetime.now(timezone.utc).isoformat())
                         period = Period()
                         period.start = now
                         flag.period = period
@@ -4560,7 +4562,7 @@ def update_patient_enrollment(patient: Union[Patient, dict, str], status: str, s
 
                     # Set an end date if a flag is present
                     if flag.period:
-                        now = FHIRDate(datetime.now(timezone.utc).isoformat())
+                        now = FHIRDateTime(datetime.now(timezone.utc).isoformat())
                         flag.period.end = now
                     else:
                         logger.debug(f"{prefix}: Flag has no period/start, cannot set end")
@@ -4573,7 +4575,7 @@ def update_patient_enrollment(patient: Union[Patient, dict, str], status: str, s
 
                     # Set an end date if a flag is present
                     if flag.period:
-                        now = FHIRDate(datetime.now(timezone.utc).isoformat())
+                        now = FHIRDateTime(datetime.now(timezone.utc).isoformat())
                         flag.period.end = now
                     else:
                         logger.debug(f"{prefix}: Flag has no period/start, cannot set end")
@@ -8923,7 +8925,7 @@ def questionnaire_response(
             response.questionnaire = canonical_url.url
             response.source = FHIR.Resources.reference_to(patient)
             response.status = "completed"
-            response.authored = FHIRDate(date.isoformat())
+            response.authored = FHIRDateTime(date.isoformat())
             response.author = FHIR.Resources.reference_to(author if author else patient)
             response.subject = FHIR.Resources.reference_to(questionnaire)
 
@@ -9081,7 +9083,7 @@ def questionnaire_response_item_answer(
                 answer.valueInteger = value
 
             elif type(value) is datetime:
-                answer.valueDateTime = FHIRDate(value.isoformat())
+                answer.valueDateTime = FHIRDateTime(value.isoformat())
 
             elif type(value) is date:
                 answer.valueDate = FHIRDate(value.isoformat())
@@ -9193,7 +9195,7 @@ def consent(
             consent = Consent()
             consent.status = "proposed"
             consent.id = uuid.uuid1().urn
-            consent.dateTime = FHIRDate(date.isoformat())
+            consent.dateTime = FHIRDateTime(date.isoformat())
             consent.patient = FHIR.Resources.reference_to(patient)
 
             # Policy
@@ -9257,7 +9259,7 @@ def contract(
             # Build it
             contract = Contract(strict=True)
             contract.status = "executed"
-            contract.issued = FHIRDate(date.isoformat())
+            contract.issued = FHIRDateTime(date.isoformat())
             contract.id = uuid.uuid1().urn
             contract.subject = [FHIR.Resources.reference_to(patient)]
 
@@ -9275,7 +9277,7 @@ def contract(
                     "http://hl7.org/fhir/ValueSet/signature-type", "1.2.840.10065.1.12.1.7", "Consent Signature"
                 )
             ]
-            signature.when = FHIRDate(date.isoformat())
+            signature.when = FHIRInstant(date.isoformat())
             signature.sigFormat = "text/plain"
             signature.data = FHIR.Resources.blob(patient_signature)
             signature.who = FHIR.Resources.reference_to(patient)
@@ -9331,7 +9333,7 @@ def related_contract(
             # Build it
             contract = Contract()
             contract.status = "executed"
-            contract.issued = FHIRDate(date.isoformat())
+            contract.issued = FHIRDateTime(date.isoformat())
             contract.id = uuid.uuid1().urn
 
             # Signer
@@ -9348,7 +9350,7 @@ def related_contract(
                     "http://hl7.org/fhir/ValueSet/signature-type", "1.2.840.10065.1.12.1.7", "Consent Signature"
                 )
             ]
-            signature.when = FHIRDate(date.isoformat())
+            signature.when = FHIRInstant(date.isoformat())
             signature.sigFormat = "text/plain"
             signature.data = FHIR.Resources.blob(related_person_signature)
             signature.who = FHIR.Resources.reference_to(related_person)
@@ -9398,7 +9400,7 @@ def composition(
             composition.id = uuid.uuid1().urn
             composition.status = "final"
             composition.subject = FHIR.Resources.reference_to(patient)
-            composition.date = FHIRDate(date.isoformat())
+            composition.date = FHIRDateTime(date.isoformat())
             composition.title = "Signature"
             composition.author = [FHIRReference({"reference": "Device/hms-dbmi-ppm-consent"})]
 

diff --git a/ppmutils/tests/test_fhir.py b/ppmutils/tests/test_fhir.py
@@ -5,7 +5,7 @@
 import uuid
 import re
 import json
-from datetime import datetime
+from datetime import datetime, timezone
 
 from ppmutils.ppm import PPM
 from ppmutils.fhir import FHIR
@@ -310,7 +310,7 @@ def test_query_enrollment_participants(self):
 
         # Check some properties
         self.assertTrue(
-            PPM.Enrollment.enum(participants[random.randint(0, len(participants))]["enrollment"])
+            PPM.Enrollment.enum(participants[random.randint(0, len(participants) - 1)]["enrollment"])
             is PPM.Enrollment.Accepted
         )
         self.assertTrue(participants[1]["email"] is not None)
@@ -362,10 +362,12 @@ def test_query_study_enrollment_participants(self):
 
         # Check some properties
         self.assertTrue(
-            PPM.Enrollment.enum(participants[random.randint(0, len(participants))]["enrollment"])
+            PPM.Enrollment.enum(participants[random.randint(0, len(participants) - 1)]["enrollment"])
             is PPM.Enrollment.Consented
         )
-        self.assertTrue(PPM.Study.enum(participants[random.randint(0, len(participants))]["study"]) is PPM.Study.RANT)
+        self.assertTrue(
+            PPM.Study.enum(participants[random.randint(0, len(participants) - 1)]["study"]) is PPM.Study.RANT
+        )
         self.assertTrue(participants[1]["email"] is not None)
 
     @responses.activate
@@ -864,7 +866,7 @@ def update_callback(request):
     def test_update_patient_deceased_1(self):
 
         # Set the deceased date
-        deceased = datetime.now()
+        deceased = datetime.now(timezone.utc)
 
         # Start a data set
         research_study, patient, flag, research_subject = FHIRData.participant(PPM.Study.NEER)
@@ -929,7 +931,7 @@ def update_callback(request):
     def test_update_patient_deceased_3(self):
 
         # Set the deceased date
-        deceased = datetime.now()
+        deceased = datetime.now(timezone.utc)
 
         # Start a data set
         research_study, patient, flag, research_subject = FHIRData.participant(PPM.Study.NEER)
@@ -1652,7 +1654,7 @@ def update_callback(request):
     def test_update_research_subject_1(self):
 
         # Set the dates
-        end = datetime.now()
+        end = datetime.now(timezone.utc)
 
         # Start a data set
         research_study, patient, flag, research_subject = FHIRData.participant(PPM.Study.NEER)
@@ -1724,8 +1726,8 @@ def test_update_research_subject_3(self):
 
         # Set a date on research subject otherwise it won't be deleted
         research_subject["period"] = {
-            "start": datetime.now().isoformat(),
-            "end": datetime.now().isoformat(),
+            "start": datetime.now(timezone.utc).isoformat(),
+            "end": datetime.now(timezone.utc).isoformat(),
         }
 
         def update_callback(request):
@@ -1755,7 +1757,7 @@ def update_callback(request):
     def test_update_ppm_research_subject_1(self):
 
         # Set the dates
-        end = datetime.now()
+        end = datetime.now(timezone.utc)
 
         # Start a data set
         research_study, patient, flag, research_subject = FHIRData.participant(PPM.Study.NEER)
@@ -1843,8 +1845,8 @@ def test_update_ppm_research_subject_3(self):
 
         # Set a date on research subject otherwise it won't be deleted
         research_subject["period"] = {
-            "start": datetime.now().isoformat(),
-            "end": datetime.now().isoformat(),
+            "start": datetime.now(timezone.utc).isoformat(),
+            "end": datetime.now(timezone.utc).isoformat(),
         }
 
         # Build the response handler
@@ -2082,7 +2084,7 @@ def create_bundle(resources, fhir_url):
         return {
             "resourceType": "Bundle",
             "id": f"{uuid.uuid4()}",
-            "meta": {"lastUpdated": datetime.now().isoformat()},
+            "meta": {"lastUpdated": datetime.now(timezone.utc).isoformat()},
             "type": "searchset",
             "total": len(resources),
             "link": [{"relation": "self", "url": fhir_url}],
@@ -2218,7 +2220,7 @@ def enrollment_flag(
         patient,
         study,
         enrollment=PPM.Enrollment.Registered.value,
-        start=datetime.now(),
+        start=datetime.now(timezone.utc),
         end=None,
     ):
         """

diff --git a/requirements.txt b/requirements.txt
@@ -1,7 +1,7 @@
 django
 boto3
 python-dateutil==2.*
-fhirclient==4.*
+fhirclient==4.2.*
 requests==2.*
 furl==2.*
 requests-auth-aws-sigv4