feat: persist patient referral form as FHIR document reference (#421)

Signed-off-by: Kathurima Kimathi <kathurimakimathi415@gmail.com>
savannahghi · Apr 9, 2024 · 98aa104 · 98aa104
1 parent 56c3750
commit 98aa104
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Showing 9 changed files with 303 additions and 28 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -45,9 +45,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 # Copy the Go binary to the production image from the builder stage.
 COPY --from=builder /app/server /server
 
-# Ensure your templates directory is correctly copied into the Docker image.
-COPY --from=builder /app/templates /app/templates
-
 # Set the working directory to where your binary and templates are.
 WORKDIR /app
 

diff --git a/pkg/clinical/application/common/defaults.go b/pkg/clinical/application/common/defaults.go
@@ -191,6 +191,9 @@ const (
 	// BreastExaminationCIELTerminologySystem is the terminology code used to represent breast examination concept.
 	// This is more a more general concept code.
 	BreastExaminationCIELTerminologySystem = "162825"
+
+	// ReferralNoteLOINCTerminologySystem is the system code used to represent referral note concept in loinc terminology system
+	ReferralNoteLOINCTerminologySystem = "57133-1"
 )
 
 // DefaultIdentifier assigns a patient a code to function as their

diff --git a/templates/referral_report_template.html → pkg/clinical/application/utils/templates.go b/templates/referral_report_template.html → pkg/clinical/application/utils/templates.go
@@ -1,3 +1,6 @@
+package utils
+
+const ReferralFormTemplate = `
 <!DOCTYPE html>
 <html lang="en">
 <head>
@@ -298,4 +301,4 @@ <h2>Referred by</h2>
     {{end}}
 </body>
 </html>
-    
+`
diff --git a/pkg/clinical/domain/complex_types_test.go b/pkg/clinical/domain/complex_types_test.go
@@ -4661,3 +4661,155 @@ func TestDocumentRelationshipTypeEnum_String(t *testing.T) {
 		})
 	}
 }
+
+func TestScreeningTypeEnum_IsValid(t *testing.T) {
+	tests := []struct {
+		name string
+		e    ScreeningTypeEnum
+		want bool
+	}{
+		{
+			name: "Valid screening type - breast cancer",
+			e:    BreastCancerScreeningTypeEnum,
+			want: true,
+		},
+		{
+			name: "Invalid screening type status",
+			e:    "invalid",
+			want: false,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := tt.e.IsValid(); got != tt.want {
+				t.Errorf("ScreeningTypeEnum.IsValid() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestScreeningTypeEnum_String(t *testing.T) {
+	tests := []struct {
+		name string
+		e    ScreeningTypeEnum
+		want string
+	}{
+		{
+			name: "Breast Cancer Screening",
+			e:    BreastCancerScreeningTypeEnum,
+			want: "BREAST_CANCER_SCREENING",
+		},
+		{
+			name: "Cervical Cancer Screening",
+			e:    CervicalCancerScreeningTypeEnum,
+			want: "CERVICAL_CANCER_SCREENING",
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := tt.e.String(); got != tt.want {
+				t.Errorf("ScreeningTypeEnum.String() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestScreeningTypeEnum_UnmarshalGQL(t *testing.T) {
+	value := BreastCancerScreeningTypeEnum
+	invalidType := ScreeningTypeEnum("invalid")
+	type args struct {
+		v interface{}
+	}
+	tests := []struct {
+		name    string
+		e       *ScreeningTypeEnum
+		args    args
+		wantErr bool
+	}{
+		{
+			name: "valid type",
+			e:    &value,
+			args: args{
+				v: "BREAST_CANCER_SCREENING",
+			},
+			wantErr: false,
+		},
+		{
+			name: "invalid type",
+			e:    &invalidType,
+			args: args{
+				v: "this is not a valid type",
+			},
+			wantErr: true,
+		},
+		{
+			name: "non string type",
+			e:    &invalidType,
+			args: args{
+				v: 1,
+			},
+			wantErr: true,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if err := tt.e.UnmarshalGQL(tt.args.v); (err != nil) != tt.wantErr {
+				t.Errorf("ScreeningTypeEnum.UnmarshalGQL() error = %v, wantErr %v", err, tt.wantErr)
+			}
+		})
+	}
+}
+
+func TestMediaScreeningTypeEnum_MarshalGQL(t *testing.T) {
+	tests := []struct {
+		name  string
+		e     ScreeningTypeEnum
+		wantW string
+	}{
+		{
+			name:  "BREAST_CANCER_SCREENING",
+			e:     BreastCancerScreeningTypeEnum,
+			wantW: strconv.Quote("BREAST_CANCER_SCREENING"),
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			w := &bytes.Buffer{}
+			tt.e.MarshalGQL(w)
+			if gotW := w.String(); gotW != tt.wantW {
+				t.Errorf("ScreeningTypeEnum.MarshalGQL() = %v, want %v", gotW, tt.wantW)
+			}
+		})
+	}
+}
+
+func TestScreeningTypeEnum_Text(t *testing.T) {
+	tests := []struct {
+		name          string
+		screeningType ScreeningTypeEnum
+		want          string
+	}{
+		{
+			name:          "Valid type - breast",
+			screeningType: BreastCancerScreeningTypeEnum,
+			want:          "Breast Cancer Screening",
+		},
+		{
+			name:          "Valid type - cervical",
+			screeningType: CervicalCancerScreeningTypeEnum,
+			want:          "Cervical Cancer Screening",
+		},
+		{
+			name:          "Invalid type",
+			screeningType: ScreeningTypeEnum("invalid"),
+			want:          "unknown screening type",
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if got := tt.screeningType.Text(); got != tt.want {
+				t.Errorf("ScreeningTypeEnum.Text() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
diff --git a/pkg/clinical/domain/document_reference.go b/pkg/clinical/domain/document_reference.go
@@ -1,5 +1,7 @@
 package domain
 
+import "github.com/savannahghi/scalarutils"
+
 // FHIRDocumentReference represents a reference to a document of any kind for any purpose.
 // It provides metadata about the document so that the document can be discovered and managed.
 // The scope of a document is any seralized object with a mime-type, so includes formal patient centric documents (CDA), cliical notes, scanned paper, and non-patient centric documents like policy text.
@@ -78,7 +80,7 @@ type FHIRDocumentReferenceInput struct {
 	Type              *FHIRCodeableConceptInput        `json:"type,omitempty"`
 	Category          []FHIRCodeableConceptInput       `json:"category,omitempty"`
 	Subject           *FHIRReferenceInput              `json:"subject,omitempty"`
-	Date              *string                          `json:"date,omitempty"`
+	Date              *scalarutils.Instant             `json:"date,omitempty"`
 	Author            []FHIRReferenceInput             `json:"author,omitempty"`
 	Authenticator     *FHIRReferenceInput              `json:"authenticator,omitempty"`
 	Custodian         *FHIRReferenceInput              `json:"custodian,omitempty"`

diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/mock/fhir_mock.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/mock/fhir_mock.go
@@ -96,8 +96,8 @@ type FHIRMock struct {
 	MockGetFHIRPatientEverythingFn        func(ctx context.Context, id string, params map[string]interface{}) (*domain.PagedFHIRResource, error)
 	MockGetFHIRServiceRequestFn           func(_ context.Context, id string) (*domain.FHIRServiceRequestRelayPayload, error)
 	MockCreateFHIRSubscriptionFn          func(_ context.Context, subscription *domain.FHIRSubscriptionInput) (*domain.FHIRSubscription, error)
-	MockCreateFHIRDocumentReferenceFn     func(ctx context.Context, subscription *domain.FHIRSubscriptionInput) (*domain.FHIRSubscription, error)
 	MockPatchFHIRServiceRequestFn         func(ctx context.Context, id string, input domain.FHIRServiceRequestInput) (*domain.FHIRServiceRequestRelayPayload, error)
+	MockCreateFHIRDocumentReferenceFn     func(ctx context.Context, documentReference *domain.FHIRDocumentReferenceInput) (*domain.FHIRDocumentReference, error)
 }
 
 // NewFHIRMock initializes a new instance of FHIR mock
@@ -2296,24 +2296,33 @@ func NewFHIRMock() *FHIRMock {
 				Channel:           domain.FHIRSubscriptionChannel{},
 			}, nil
 		},
-		MockCreateFHIRDocumentReferenceFn: func(ctx context.Context, subscription *domain.FHIRSubscriptionInput) (*domain.FHIRSubscription, error) {
-			resourceID := uuid.New().String()
-			return &domain.FHIRSubscription{
-				ID:                &resourceID,
+		MockCreateFHIRDocumentReferenceFn: func(ctx context.Context, documentReference *domain.FHIRDocumentReferenceInput) (*domain.FHIRDocumentReference, error) {
+			resourceID := gofakeit.UUID()
+			return &domain.FHIRDocumentReference{
+				ID:                resourceID,
 				Meta:              &domain.FHIRMeta{},
 				ImplicitRules:     new(string),
 				Language:          new(string),
 				Text:              &domain.FHIRNarrative{},
-				Extension:         []*domain.Extension{},
-				ModifierExtension: []*domain.Extension{},
-				Identifier:        []*domain.FHIRIdentifier{},
+				Extension:         []domain.FHIRExtension{},
+				ModifierExtension: []domain.FHIRExtension{},
+				MasterIdentifier:  &domain.FHIRIdentifier{},
+				Identifier:        []domain.FHIRIdentifier{},
 				Status:            "",
-				Contact:           []domain.FHIRContactPoint{},
-				End:               new(string),
-				Reason:            "",
-				Criteria:          "",
-				Error:             new(string),
-				Channel:           domain.FHIRSubscriptionChannel{},
+				Type: &domain.FHIRCodeableConcept{
+					ID: &resourceID,
+				},
+				Category:      []domain.FHIRCodeableConcept{},
+				Subject:       &domain.FHIRReference{},
+				Date:          new(string),
+				Author:        []domain.FHIRReference{},
+				Authenticator: &domain.FHIRReference{},
+				Custodian:     &domain.FHIRReference{},
+				RelatesTo:     []domain.FHIRDocumentReferenceRelatesTo{},
+				Description:   "",
+				SecurityLabel: []domain.FHIRCodeableConcept{},
+				Content:       []domain.FHIRDocumentReferenceContent{},
+				Context:       &domain.FHIRDocumentReferenceContext{},
 			}, nil
 		},
 	}
@@ -2685,8 +2694,8 @@ func (fh *FHIRMock) CreateFHIRSubscription(ctx context.Context, subscription *do
 }
 
 // CreateFHIRDocumentReference mocks the implementation of creating a FHIR document reference
-func (fh *FHIRMock) CreateFHIRDocumentReference(ctx context.Context, subscription *domain.FHIRSubscriptionInput) (*domain.FHIRSubscription, error) {
-	return fh.MockCreateFHIRSubscriptionFn(ctx, subscription)
+func (fh *FHIRMock) CreateFHIRDocumentReference(ctx context.Context, documentReference *domain.FHIRDocumentReferenceInput) (*domain.FHIRDocumentReference, error) {
+	return fh.MockCreateFHIRDocumentReferenceFn(ctx, documentReference)
 }
 
 // PatchFHIRServiceRequest mocks the implementation of mocking patching service request

diff --git a/pkg/clinical/repository/repository.go b/pkg/clinical/repository/repository.go
@@ -28,6 +28,7 @@ type FHIR interface {
 	FHIRRiskAssessment
 	FHIRDiagnosticReport
 	FHIRSubscription
+	FHIRDocumentReference
 }
 
 type FHIROrganization interface {

diff --git a/pkg/clinical/usecases/clinical/referral_report.go b/pkg/clinical/usecases/clinical/referral_report.go
@@ -9,8 +9,11 @@ import (
 	"time"
 
 	"github.com/SebastiaanKlippert/go-wkhtmltopdf"
+	"github.com/savannahghi/clinical/pkg/clinical/application/common"
 	"github.com/savannahghi/clinical/pkg/clinical/application/common/helpers"
+	"github.com/savannahghi/clinical/pkg/clinical/application/dto"
 	"github.com/savannahghi/clinical/pkg/clinical/application/utils"
+	"github.com/savannahghi/clinical/pkg/clinical/domain"
 	"github.com/savannahghi/scalarutils"
 )
 
@@ -162,14 +165,10 @@ func (c *UseCasesClinicalImpl) GenerateReferralReportPDF(ctx context.Context, se
 		Footer:         Footer{},
 	}
 
-	tmpl, err := template.ParseFiles("templates/referral_report_template.html")
-	if err != nil {
-		utils.ReportErrorToSentry(err)
-		return nil, err
-	}
-
 	var htmlBuffer bytes.Buffer
 
+	tmpl := template.Must(template.New("ReferralFormTemplate").Parse(utils.ReferralFormTemplate))
+
 	err = tmpl.Execute(&htmlBuffer, data)
 	if err != nil {
 		utils.ReportErrorToSentry(err)
@@ -197,11 +196,79 @@ func (c *UseCasesClinicalImpl) GenerateReferralReportPDF(ctx context.Context, se
 	currentTime := time.Now().Format("20060102T150405")
 	filename := fmt.Sprintf("%s_%s.pdf", patientData.Name, currentTime)
 
-	_, err = c.infrastructure.Upload.UploadMedia(ctx, filename, bytes.NewReader(pdfBytes), "")
+	result, err := c.infrastructure.Upload.UploadMedia(ctx, filename, bytes.NewReader(pdfBytes), "")
+	if err != nil {
+		utils.ReportErrorToSentry(err)
+		return nil, err
+	}
+
+	_, err = c.CreateDocumentReference(ctx, serviceRequest, result)
 	if err != nil {
 		utils.ReportErrorToSentry(err)
 		return nil, err
 	}
 
 	return pdfBytes, nil
 }
+
+// CreateDocumentReference is a helper method to abstract the creation of a document reference
+func (c *UseCasesClinicalImpl) CreateDocumentReference(ctx context.Context, serviceRequest *domain.FHIRServiceRequestRelayPayload, result *dto.Media) (bool, error) {
+	concept, err := c.GetConcept(ctx, dto.TerminologySourceLOINC, common.ReferralNoteLOINCTerminologySystem)
+	if err != nil {
+		utils.ReportErrorToSentry(err)
+		return true, err
+	}
+
+	finalDocStatus := domain.CompositionStatusEnumFinal
+	status := domain.DocumentReferenceStatusEnumCurrent
+	instant := scalarutils.Instant(time.Now().Format(time.RFC3339))
+	title := fmt.Sprintf("%s's Referral report", serviceRequest.Resource.Subject.Display)
+	serviceRequestReference := fmt.Sprintf("ServiceRequest/%s", *serviceRequest.Resource.ID)
+
+	documentReference := &domain.FHIRDocumentReferenceInput{
+		Meta:       &domain.FHIRMetaInput{},
+		Identifier: []domain.FHIRIdentifierInput{},
+		Status:     status,
+		DocStatus:  &finalDocStatus,
+		Type: &domain.FHIRCodeableConceptInput{
+			Coding: []*domain.FHIRCodingInput{
+				{
+					System:  (*scalarutils.URI)(&concept.URL),
+					Code:    scalarutils.Code(concept.ID),
+					Display: concept.DisplayName,
+				},
+			},
+			Text: concept.DisplayName,
+		},
+		Subject: &domain.FHIRReferenceInput{
+			ID:        serviceRequest.Resource.Subject.ID,
+			Reference: serviceRequest.Resource.Subject.Reference,
+		},
+		Date: &instant,
+		Content: []domain.FHIRDocumentReferenceContent{
+			{
+				Attachment: domain.FHIRAttachment{
+					ContentType: (*scalarutils.Code)(&result.ContentType),
+					URL:         (*scalarutils.URL)(&result.SignedURL),
+					Title:       &title,
+				},
+			},
+		},
+		Context: &domain.FHIRDocumentReferenceContext{
+			Related: []domain.Reference{
+				{
+					Reference: serviceRequestReference,
+					Type:      "ServiceRequest",
+				},
+			},
+		},
+	}
+
+	_, err = c.infrastructure.FHIR.CreateFHIRDocumentReference(ctx, documentReference)
+	if err != nil {
+		utils.ReportErrorToSentry(err)
+		return true, err
+	}
+
+	return false, nil
+}