feat: create test result FHIR observation (#86)

savannahghi · Mar 28, 2022 · f44e255 · f44e255
1 parent 96fc9e3
commit f44e255
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Showing 3 changed files with 124 additions and 22 deletions.
diff --git a/pkg/clinical/application/dto/pubsub.go b/pkg/clinical/application/dto/pubsub.go
@@ -84,3 +84,19 @@ type CreateMedicationPubSubMessage struct {
 type MedicationDrug struct {
 	ConceptID *string `json:"conceptId"`
 }
+
+// CreatePatientTestResultPubSubMessage models details that are published to the test results topic
+type CreatePatientTestResultPubSubMessage struct {
+	PatientID      string     `json:"patientID"`
+	OrganizationID string     `json:"organizationID"`
+	Name           string     `json:"name"`
+	ConceptID      *string    `json:"conceptId"`
+	Date           time.Time  `json:"date"`
+	Result         TestResult `json:"result"`
+}
+
+// TestResult ...
+type TestResult struct {
+	Name      string  `json:"name"`
+	ConceptID *string `json:"conceptId"`
+}
diff --git a/pkg/clinical/domain/concept.go b/pkg/clinical/domain/concept.go
@@ -4,26 +4,26 @@ import "time"
 
 // Concept models a concept type from OpenConceptLab
 type Concept struct {
-	ConceptClass     string     `json:"concept_class"`
-	DataType         string     `json:"datatype"`
-	DisplayLocale    string     `json:"display_locale"`
-	DisplayName      string     `json:"display_name"`
-	ExternalID       string     `json:"external_id"`
-	ID               string     `json:"id"`
-	IsLatestVersion  bool       `json:"is_latest_version"`
-	Locale           *string    `json:"locale"`
-	Owner            string     `json:"owner"`
-	OwnerType        string     `json:"owner_type"`
-	OwnerURL         string     `json:"owner_url"`
-	Retired          bool       `json:"retired"`
-	Source           string     `json:"source"`
-	Type             string     `json:"type"`
-	UpdateComment    string     `json:"update_comment"`
-	URL              string     `json:"url"`
-	UUID             string     `json:"uuid"`
-	Version          string     `json:"version"`
-	VersionCreatedBy string     `json:"version_created_by"`
-	VersionCreatedOn *time.Time `json:"version_created_on"`
-	VersionURL       string     `json:"version_url"`
-	VersionsURL      string     `json:"versions_url"`
+	ConceptClass     string     `mapstructure:"concept_class" json:"concept_class"`
+	DataType         string     `mapstructure:"datatype" json:"datatype"`
+	DisplayLocale    string     `mapstructure:"display_locale" json:"display_locale"`
+	DisplayName      string     `mapstructure:"display_name" json:"display_name"`
+	ExternalID       string     `mapstructure:"external_id" json:"external_id"`
+	ID               string     `mapstructure:"id" json:"id"`
+	IsLatestVersion  bool       `mapstructure:"is_latest_version" json:"is_latest_version"`
+	Locale           *string    `mapstructure:"locale" json:"locale"`
+	Owner            string     `mapstructure:"owner" json:"owner"`
+	OwnerType        string     `mapstructure:"owner_type" json:"owner_type"`
+	OwnerURL         string     `mapstructure:"owner_url" json:"owner_url"`
+	Retired          bool       `mapstructure:"retired" json:"retired"`
+	Source           string     `mapstructure:"source" json:"source"`
+	Type             string     `mapstructure:"type" json:"type"`
+	UpdateComment    string     `mapstructure:"update_comment" json:"update_comment"`
+	URL              string     `mapstructure:"url" json:"url"`
+	UUID             string     `mapstructure:"uuid" json:"uuid"`
+	Version          string     `mapstructure:"version" json:"version"`
+	VersionCreatedBy string     `mapstructure:"version_created_by" json:"version_created_by"`
+	VersionCreatedOn *time.Time `mapstructure:"version_created_on" json:"version_created_on"`
+	VersionURL       string     `mapstructure:"version_url" json:"version_url"`
+	VersionsURL      string     `mapstructure:"versions_url" json:"versions_url"`
 }
diff --git a/pkg/clinical/infrastructure/services/pubsub/subscriber.go b/pkg/clinical/infrastructure/services/pubsub/subscriber.go
@@ -428,6 +428,92 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			return
 		}
 
+	case ps.AddPubSubNamespace(common.TestResultTopicName, ClinicalServiceName):
+		var data dto.CreatePatientTestResultPubSubMessage
+		err := json.Unmarshal(message.Message.Data, &data)
+		if err != nil {
+			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
+				Err:     err,
+				Message: err.Error(),
+			}, http.StatusBadRequest)
+			return
+		}
+
+		response, err := ps.ocl.GetConcept(
+			ctx,
+			"CIEL",
+			"CIEL",
+			*data.ConceptID,
+			false,
+			false,
+		)
+		if err != nil {
+			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
+				Err:     err,
+				Message: err.Error(),
+			}, http.StatusBadRequest)
+			return
+		}
+
+		var ConceptPayload domain.Concept
+		err = mapstructure.Decode(response, &ConceptPayload)
+		if err != nil {
+			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
+				Err:     err,
+				Message: err.Error(),
+			}, http.StatusBadRequest)
+			return
+		}
+
+		year, month, day := data.Date.Date()
+		system := "http://terminology.hl7.org/CodeSystem/observation-category"
+		subjectReference := fmt.Sprintf("Patient/%v", data.PatientID)
+		status := domain.ObservationStatusEnumPreliminary
+		input := domain.FHIRObservationInput{
+			Status: &status,
+			Category: []*domain.FHIRCodeableConceptInput{
+				{
+					Coding: []*domain.FHIRCodingInput{
+						{
+							System:  (*scalarutils.URI)(&system),
+							Code:    "laboratory",
+							Display: "Laboratory",
+						},
+					},
+					Text: "Laboratory",
+				},
+			},
+
+			Code: domain.FHIRCodeableConceptInput{
+				Coding: []*domain.FHIRCodingInput{
+					{
+						System:  (*scalarutils.URI)(&ConceptPayload.URL),
+						Code:    scalarutils.Code(ConceptPayload.ID),
+						Display: ConceptPayload.DisplayName,
+					},
+				},
+				Text: ConceptPayload.DisplayName,
+			},
+			ValueString: &data.Result.Name,
+			EffectiveDateTime: &scalarutils.Date{
+				Year:  year,
+				Month: int(month),
+				Day:   day,
+			},
+			Subject: &domain.FHIRReferenceInput{
+				Reference: &subjectReference,
+				Display:   data.PatientID,
+			},
+		}
+
+		_, err = ps.fhir.CreateFHIRObservation(ctx, input)
+		if err != nil {
+			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
+				Err:     err,
+				Message: err.Error(),
+			}, http.StatusBadRequest)
+			return
+		}
 	}
 
 	resp := map[string]string{"Status": "Success"}