chore: change pubsub to v2, remove encounter check

savannahghi · Apr 25, 2023 · b0b755e · b0b755e
1 parent 0474090
commit b0b755e
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Showing 4 changed files with 28 additions and 33 deletions.
diff --git a/pkg/clinical/infrastructure/services/pubsub/service.go b/pkg/clinical/infrastructure/services/pubsub/service.go
@@ -16,6 +16,8 @@ const (
 
 	// TestTopicName is a topic that is used for testing purposes
 	TestTopicName = "pubsub.testing.topic"
+
+	TopicVersion = "v2"
 )
 
 // BaseExtension is an interface that represents some methods in base
@@ -66,7 +68,7 @@ func (ps ServicePubSubMessaging) AddPubSubNamespace(topicName, serviceName strin
 		serviceName,
 		topicName,
 		environment,
-		common.TopicVersion,
+		TopicVersion,
 	)
 }
 
@@ -102,7 +104,7 @@ func (ps ServicePubSubMessaging) PublishToPubsub(
 		topicID,
 		environment,
 		common.ClinicalServiceName,
-		common.TopicVersion,
+		TopicVersion,
 		payload,
 	)
 }

diff --git a/pkg/clinical/infrastructure/services/pubsub/service_test.go b/pkg/clinical/infrastructure/services/pubsub/service_test.go
@@ -73,7 +73,7 @@ func TestServicePubSubMessaging_AddPubSubNamespace(t *testing.T) {
 				common.ClinicalServiceName,
 				topicName,
 				environment,
-				common.TopicVersion,
+				pubsubmessaging.TopicVersion,
 			),
 			wantErr: false,
 		},

diff --git a/pkg/clinical/usecases/clinical/patient.go b/pkg/clinical/usecases/clinical/patient.go
@@ -108,14 +108,6 @@ func (c *UseCasesClinicalImpl) GetMedicalData(ctx context.Context, patientID str
 					continue
 				}
 
-				if edge.Encounter == nil {
-					continue
-				}
-
-				if edge.Encounter.ID == nil {
-					continue
-				}
-
 				if edge.Code == nil {
 					continue
 				}
@@ -217,14 +209,6 @@ func hasNilInObservation(observation *domain.FHIRObservationRelayEdge) bool {
 		return true
 	}
 
-	if observation.Node.Encounter == nil {
-		return true
-	}
-
-	if observation.Node.Encounter.ID == nil {
-		return true
-	}
-
 	return false
 }
 
@@ -242,11 +226,14 @@ func mapFHIRMedicationStatementToMedicationStatementDTO(fhirAllergyIntolerance *
 
 func mapFHIRAllergyIntoleranceToAllergyIntoleranceDTO(fhirAllergyIntolerance domain.FHIRAllergyIntolerance) *dto.Allergy {
 	allergyIntolerance := &dto.Allergy{
-		ID:          *fhirAllergyIntolerance.ID,
-		PatientID:   *fhirAllergyIntolerance.Patient.ID,
-		EncounterID: *fhirAllergyIntolerance.Encounter.ID,
-		Code:        string(fhirAllergyIntolerance.Code.Coding[0].Code),
-		System:      string(*fhirAllergyIntolerance.Code.Coding[0].System),
+		ID:        *fhirAllergyIntolerance.ID,
+		PatientID: *fhirAllergyIntolerance.Patient.ID,
+		Code:      string(fhirAllergyIntolerance.Code.Coding[0].Code),
+		System:    string(*fhirAllergyIntolerance.Code.Coding[0].System),
+	}
+
+	if fhirAllergyIntolerance.Encounter != nil && fhirAllergyIntolerance.Encounter.ID != nil {
+		allergyIntolerance.EncounterID = *fhirAllergyIntolerance.Encounter.ID
 	}
 
 	if fhirAllergyIntolerance.OnsetPeriod != nil {
@@ -322,14 +309,19 @@ func mapFHIRObservationToObservationDTO(fhirObservation *domain.FHIRObservation)
 		value = fmt.Sprintf("%v - %v", fhirObservation.ValuePeriod.Start, fhirObservation.ValuePeriod.End)
 	}
 
-	return &dto.Observation{
-		ID:          *fhirObservation.ID,
-		Status:      dto.ObservationStatus(*fhirObservation.Status),
-		Name:        fhirObservation.Code.Coding[0].Display,
-		Value:       value,
-		PatientID:   *fhirObservation.Subject.ID,
-		EncounterID: *fhirObservation.Encounter.ID,
+	obs := &dto.Observation{
+		ID:        *fhirObservation.ID,
+		Status:    dto.ObservationStatus(*fhirObservation.Status),
+		Name:      fhirObservation.Code.Coding[0].Display,
+		Value:     value,
+		PatientID: *fhirObservation.Subject.ID,
+	}
+
+	if fhirObservation.Encounter != nil && fhirObservation.Encounter.ID != nil {
+		obs.EncounterID = *fhirObservation.Encounter.ID
 	}
+
+	return obs
 }
 
 // CreatePatient creates a new patient

diff --git a/pkg/clinical/usecases/clinical/timeline.go b/pkg/clinical/usecases/clinical/timeline.go
@@ -3,6 +3,7 @@ package clinical
 import (
 	"context"
 	"fmt"
+	"github.com/savannahghi/clinical/pkg/clinical/application/common/helpers"
 	"sync"
 
 	linq "github.com/ahmetb/go-linq/v3"
@@ -125,11 +126,11 @@ func (c *UseCasesClinicalImpl) PatientTimeline(ctx context.Context, patientID st
 				continue
 			}
 
-			if edge.Node.EffectiveDateTime == nil {
+			if edge.Node.EffectiveInstant == nil {
 				continue
 			}
 
-			instant := edge.Node.EffectiveDateTime.AsTime()
+			instant := helpers.ParseDate(string(*edge.Node.EffectiveInstant))
 			date, err := scalarutils.NewDate(instant.Day(), int(instant.Month()), instant.Year())
 
 			if err != nil {