feat: record mammography result

- This API is used to record mammography results Link to documentation: [https://savannahghi.atlassian.net/wiki/spaces/OHE/pages/468025506/API+Documentation#Record-Mammography-Result] Signed-off-by: Kathurima Kimathi <kathurimakimathi415@gmail.com>
savannahghi · Feb 5, 2024 · 4f926da · 4f926da
1 parent f08bec5
commit 4f926da
Show file tree

Hide file tree

Showing 16 changed files with 758 additions and 46 deletions.
diff --git a/pkg/clinical/application/common/defaults.go b/pkg/clinical/application/common/defaults.go
@@ -157,6 +157,12 @@ const (
 
 	// CIELTerminologySystem is the identity of ciel terminology system
 	CIELTerminologySystem = "https://CIELterminology.org"
+
+	// MammogramTerminologyCode is the terminology code used to represent mammogram results.
+	MammogramTerminologyCode = "163591"
+
+	// BenignNeoplasmOfBreastOfSkinTerminologyCode is the terminology code used to represent benign of skin results.
+	BenignNeoplasmOfBreastOfSkinTerminologyCode = "147661"
 )
 
 // DefaultIdentifier assigns a patient a code to function as their

diff --git a/pkg/clinical/application/dto/diagnostic_report_output.go b/pkg/clinical/application/dto/diagnostic_report_output.go
@@ -1,5 +1,12 @@
 package dto
 
-type DiagnosticReportOutput struct {
-	ID string `json:"id,omitempty"`
+type DiagnosticReport struct {
+	ID          string            `json:"id,omitempty"`
+	Status      ObservationStatus `json:"status,omitempty"`
+	PatientID   string            `json:"patientID,omitempty"`
+	EncounterID string            `json:"encounterID,omitempty"`
+	Issued      string            `json:"issued,omitempty"`
+	Result      []*Observation    `json:"result,omitempty"`
+	Media       []*Media          `json:"media,omitempty"`
+	Conclusion  string            `json:"conclusion,omitempty"`
 }
diff --git a/pkg/clinical/application/dto/input.go b/pkg/clinical/application/dto/input.go
@@ -1,6 +1,7 @@
 package dto
 
 import (
+	"io"
 	"mime/multipart"
 
 	"github.com/go-playground/validator"
@@ -31,7 +32,7 @@ type EncounterInput struct {
 type ObservationInput struct {
 	Status      ObservationStatus `json:"status,omitempty" validate:"required"`
 	EncounterID string            `json:"encounterID,omitempty" validate:"required"`
-	Value       string            `json:"value,omitempty" validate:"required"`
+	Value       string            `json:"value,omitempty"`
 }
 
 func (o ObservationInput) Validate() error {
@@ -222,3 +223,19 @@ type Expression struct {
 	Expression  *string     `json:"expression,omitempty"`
 	Reference   *string     `json:"reference,omitempty"`
 }
+
+// DiagnosticReportInput represents the data class used to provide diagnostic report information
+type DiagnosticReportInput struct {
+	EncounterID string                             `json:"encounterID,omitempty"  validate:"required"`
+	Note        string                             `json:"note,omitempty"`
+	Attachment  map[string][]*multipart.FileHeader `form:"attachment" json:"attachment"  validate:"required"`
+	Findings    string                             `json:"findings,omitempty" validate:"required"`
+	File        io.Reader                          `json:"file,omitempty"`
+}
+
+func (d DiagnosticReportInput) Validate() error {
+	v := validator.New()
+	err := v.Struct(d)
+
+	return err
+}
diff --git a/pkg/clinical/application/extensions/mock/extension_mock.go b/pkg/clinical/application/extensions/mock/extension_mock.go
@@ -92,6 +92,7 @@ func NewFakeBaseExtensionMock() *FakeBaseExtension {
 		MockGetTenantIdentifiersFn: func(ctx context.Context) (*dto.TenantIdentifiers, error) {
 			return &dto.TenantIdentifiers{
 				OrganizationID: uuid.New().String(),
+				FacilityID:     uuid.New().String(),
 			}, nil
 		},
 		MockVerifyPubSubJWTAndDecodePayloadFn: func(w http.ResponseWriter, r *http.Request) (*pubsubtools.PubSubPayload, error) {

diff --git a/pkg/clinical/domain/diagnostic_report.go b/pkg/clinical/domain/diagnostic_report.go
@@ -1,40 +1,81 @@
 package domain
 
-// DiagnosticReport is documented here http://hl7.org/fhir/StructureDefinition/DiagnosticReport
-type DiagnosticReport struct {
-	ID                 *string                    `json:"id,omitempty"`
-	Meta               *FHIRMeta                  `json:"meta,omitempty"`
-	ImplicitRules      *string                    `json:"implicitRules,omitempty"`
-	Language           *string                    `json:"language,omitempty"`
-	Text               *FHIRNarrative             `json:"text,omitempty"`
-	Extension          []*Extension               `json:"extension,omitempty"`
-	ModifierExtension  []*Extension               `json:"modifierExtension,omitempty"`
-	Identifier         []*FHIRIdentifier          `json:"identifier,omitempty"`
-	BasedOn            []*FHIRReference           `json:"basedOn,omitempty"`
-	Status             DiagnosticReportStatusEnum `json:"status"`
-	Category           []*FHIRCodeableConcept     `json:"category,omitempty"`
-	Code               FHIRCodeableConcept        `json:"code"`
-	Subject            *FHIRReference             `json:"subject,omitempty"`
-	Encounter          *FHIRReference             `json:"encounter,omitempty"`
-	EffectiveDateTime  *string                    `json:"effectiveDateTime,omitempty"`
-	EffectivePeriod    *FHIRPeriod                `json:"effectivePeriod,omitempty"`
-	Issued             *string                    `json:"issued,omitempty"`
-	Performer          []*FHIRReference           `json:"performer,omitempty"`
-	ResultsInterpreter []*FHIRReference           `json:"resultsInterpreter,omitempty"`
-	Specimen           []*FHIRReference           `json:"specimen,omitempty"`
-	Result             []*FHIRReference           `json:"result,omitempty"`
-	ImagingStudy       []*FHIRReference           `json:"imagingStudy,omitempty"`
-	Media              []*DiagnosticReportMedia   `json:"media,omitempty"`
-	Conclusion         *string                    `json:"conclusion,omitempty"`
-	ConclusionCode     []*FHIRCodeableConcept     `json:"conclusionCode,omitempty"`
-	PresentedForm      []*FHIRAttachment          `json:"presentedForm,omitempty"`
+import "github.com/savannahghi/scalarutils"
+
+// FHIRDiagnosticReport is documented here http://hl7.org/fhir/StructureDefinition/DiagnosticReport
+type FHIRDiagnosticReport struct {
+	ID                 *string                      `json:"id,omitempty"`
+	Meta               *FHIRMeta                    `json:"meta,omitempty"`
+	ImplicitRules      *string                      `json:"implicitRules,omitempty"`
+	Language           *string                      `json:"language,omitempty"`
+	Text               *FHIRNarrative               `json:"text,omitempty"`
+	Extension          []*Extension                 `json:"extension,omitempty"`
+	ModifierExtension  []*Extension                 `json:"modifierExtension,omitempty"`
+	Identifier         []*FHIRIdentifier            `json:"identifier,omitempty"`
+	BasedOn            []*FHIRReference             `json:"basedOn,omitempty"`
+	Status             DiagnosticReportStatusEnum   `json:"status"`
+	Category           []*FHIRCodeableConcept       `json:"category,omitempty"`
+	Code               FHIRCodeableConcept          `json:"code"`
+	Subject            *FHIRReference               `json:"subject,omitempty"`
+	Encounter          *FHIRReference               `json:"encounter,omitempty"`
+	EffectiveDateTime  *scalarutils.DateTime        `json:"effectiveDateTime,omitempty"`
+	EffectivePeriod    *FHIRPeriod                  `json:"effectivePeriod,omitempty"`
+	Issued             *string                      `json:"issued,omitempty"`
+	Performer          []*FHIRReference             `json:"performer,omitempty"`
+	ResultsInterpreter []*FHIRReference             `json:"resultsInterpreter,omitempty"`
+	Specimen           []*FHIRReference             `json:"specimen,omitempty"`
+	Result             []*FHIRReference             `json:"result,omitempty"`
+	ImagingStudy       []*FHIRReference             `json:"imagingStudy,omitempty"`
+	Media              []*FHIRDiagnosticReportMedia `json:"media,omitempty"`
+	Conclusion         *string                      `json:"conclusion,omitempty"`
+	ConclusionCode     []*FHIRCodeableConcept       `json:"conclusionCode,omitempty"`
+	PresentedForm      []*FHIRAttachment            `json:"presentedForm,omitempty"`
 }
 
-// DiagnosticReportMedia represents the key images associated with this report
-type DiagnosticReportMedia struct {
+// FHIRDiagnosticReportMedia represents the key images associated with this report
+type FHIRDiagnosticReportMedia struct {
 	ID                *string        `json:"id,omitempty"`
 	Extension         []*Extension   `json:"extension,omitempty"`
 	ModifierExtension []*Extension   `json:"modifierExtension,omitempty"`
 	Comment           *string        `json:"comment,omitempty"`
 	Link              *FHIRReference `json:"link"`
 }
+
+// FHIRDiagnosticReportInput is documented here http://hl7.org/fhir/StructureDefinition/DiagnosticReport
+type FHIRDiagnosticReportInput struct {
+	ID                 *string                           `json:"id,omitempty"`
+	Meta               *FHIRMetaInput                    `json:"meta,omitempty"`
+	ImplicitRules      *string                           `json:"implicitRules,omitempty"`
+	Language           *string                           `json:"language,omitempty"`
+	Text               *FHIRNarrativeInput               `json:"text,omitempty"`
+	Extension          []*FHIRExtension                  `json:"extension,omitempty"`
+	ModifierExtension  []*FHIRExtension                  `json:"modifierExtension,omitempty"`
+	Identifier         []*FHIRIdentifierInput            `json:"identifier,omitempty"`
+	BasedOn            []*FHIRReferenceInput             `json:"basedOn,omitempty"`
+	Status             DiagnosticReportStatusEnum        `json:"status"`
+	Category           []*FHIRCodeableConceptInput       `json:"category,omitempty"`
+	Code               FHIRCodeableConceptInput          `json:"code"`
+	Subject            *FHIRReferenceInput               `json:"subject,omitempty"`
+	Encounter          *FHIRReferenceInput               `json:"encounter,omitempty"`
+	EffectiveDateTime  *scalarutils.DateTime             `json:"effectiveDateTime,omitempty"`
+	EffectivePeriod    *FHIRPeriodInput                  `json:"effectivePeriod,omitempty"`
+	Issued             *string                           `json:"issued,omitempty"`
+	Performer          []*FHIRReferenceInput             `json:"performer,omitempty"`
+	ResultsInterpreter []*FHIRReferenceInput             `json:"resultsInterpreter,omitempty"`
+	Specimen           []*FHIRReferenceInput             `json:"specimen,omitempty"`
+	Result             []*FHIRReferenceInput             `json:"result,omitempty"`
+	ImagingStudy       []*FHIRReferenceInput             `json:"imagingStudy,omitempty"`
+	Media              []*FHIRDiagnosticReportMediaInput `json:"media,omitempty"`
+	Conclusion         *string                           `json:"conclusion,omitempty"`
+	ConclusionCode     []*FHIRCodeableConceptInput       `json:"conclusionCode,omitempty"`
+	PresentedForm      []*FHIRAttachmentInput            `json:"presentedForm,omitempty"`
+}
+
+// FHIRDiagnosticReportMediaInput represents the key images associated with this report
+type FHIRDiagnosticReportMediaInput struct {
+	ID                *string             `json:"id,omitempty"`
+	Extension         []*FHIRExtension    `json:"extension,omitempty"`
+	ModifierExtension []*FHIRExtension    `json:"modifierExtension,omitempty"`
+	Comment           *string             `json:"comment,omitempty"`
+	Link              *FHIRReferenceInput `json:"link"`
+}
diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir.go
@@ -39,6 +39,7 @@ const (
 	consentResourceType               = "Consent"
 	questionnaireResponseResourceType = "QuestionnaireResponse"
 	riskAssessmentResourceType        = "RiskAssessment"
+	diagnosticReportResourceType      = "DiagnosticReport"
 )
 
 // Dataset ...
@@ -1809,3 +1810,20 @@ func (fh StoreImpl) GetFHIRQuestionnaire(_ context.Context, id string) (*domain.
 
 	return payload, nil
 }
+
+// CreateFHIRDiagnosticReport is used to create a diagnostic report resource for a patient
+func (fh StoreImpl) CreateFHIRDiagnosticReport(_ context.Context, input *domain.FHIRDiagnosticReportInput) (*domain.FHIRDiagnosticReport, error) {
+	payload, err := converterandformatter.StructToMap(input)
+	if err != nil {
+		return nil, fmt.Errorf("unable to turn %s input into a map: %w", diagnosticReportResourceType, err)
+	}
+
+	resource := &domain.FHIRDiagnosticReport{}
+
+	err = fh.Dataset.CreateFHIRResource(diagnosticReportResourceType, payload, resource)
+	if err != nil {
+		return nil, fmt.Errorf("unable to create %s resource: %w", diagnosticReportResourceType, err)
+	}
+
+	return resource, nil
+}
diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir_unit_test.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir_unit_test.go
@@ -4872,3 +4872,54 @@ func TestStoreImpl_GetFHIRQuestionnaire(t *testing.T) {
 		})
 	}
 }
+
+func TestStoreImpl_CreateFHIRDiagnosticReport(t *testing.T) {
+	ID := gofakeit.UUID()
+	type args struct {
+		in0   context.Context
+		input *domain.FHIRDiagnosticReportInput
+	}
+	tests := []struct {
+		name    string
+		args    args
+		want    *domain.FHIRDiagnosticReport
+		wantErr bool
+	}{
+		{
+			name: "Happy case: create diagnostic report",
+			args: args{
+				input: &domain.FHIRDiagnosticReportInput{
+					ID: &ID,
+				},
+			},
+			wantErr: false,
+		},
+		{
+			name: "Sad case: unable to create diagnostic report",
+			args: args{
+				input: &domain.FHIRDiagnosticReportInput{
+					ID: &ID,
+				},
+			},
+			wantErr: true,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fakeDataset := fakeDataset.NewFakeFHIRRepositoryMock()
+			fh := FHIR.NewFHIRStoreImpl(fakeDataset)
+
+			if tt.name == "Sad case: unable to create diagnostic report" {
+				fakeDataset.MockCreateFHIRResourceFn = func(resourceType string, payload map[string]interface{}, resource interface{}) error {
+					return fmt.Errorf("an error ocurred")
+				}
+			}
+
+			_, err := fh.CreateFHIRDiagnosticReport(tt.args.in0, tt.args.input)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("StoreImpl.CreateFHIRDiagnosticReport() error = %v, wantErr %v", err, tt.wantErr)
+				return
+			}
+		})
+	}
+}
diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/mock/fhir_mock.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/mock/fhir_mock.go
@@ -87,6 +87,7 @@ type FHIRMock struct {
 	MockCreateFHIRQuestionnaireResponseFn func(ctx context.Context, input *domain.FHIRQuestionnaireResponse) (*domain.FHIRQuestionnaireResponse, error)
 	MockCreateFHIRRiskAssessmentFn        func(ctx context.Context, input *domain.FHIRRiskAssessmentInput) (*domain.FHIRRiskAssessmentRelayPayload, error)
 	MockGetFHIRQuestionnaireFn            func(ctx context.Context, id string) (*domain.FHIRQuestionnaireRelayPayload, error)
+	MockCreateFHIRDiagnosticReportFn      func(_ context.Context, input *domain.FHIRDiagnosticReportInput) (*domain.FHIRDiagnosticReport, error)
 }
 
 // NewFHIRMock initializes a new instance of FHIR mock
@@ -1572,10 +1573,11 @@ func NewFHIRMock() *FHIRMock {
 			return &domain.FHIRMedicationRelayPayload{}, nil
 		},
 		MockCreateFHIRMediaFn: func(ctx context.Context, input domain.FHIRMedia) (*domain.FHIRMedia, error) {
-			id := uuid.New().String()
+			id := "1"
 			url := gofakeit.URL()
 			title := gofakeit.BeerName()
 			return &domain.FHIRMedia{
+				ID:     &id,
 				Status: "",
 				Subject: &domain.FHIRReferenceInput{
 					ID: &id,
@@ -1982,6 +1984,40 @@ func NewFHIRMock() *FHIRMock {
 			}
 			return &domain.FHIRQuestionnaireRelayPayload{Resource: resource}, nil
 		},
+		MockCreateFHIRDiagnosticReportFn: func(_ context.Context, input *domain.FHIRDiagnosticReportInput) (*domain.FHIRDiagnosticReport, error) {
+			ID := "1234"
+			return &domain.FHIRDiagnosticReport{
+				ID:                new(string),
+				Meta:              &domain.FHIRMeta{},
+				ImplicitRules:     new(string),
+				Language:          new(string),
+				Text:              &domain.FHIRNarrative{},
+				Extension:         []*domain.Extension{},
+				ModifierExtension: []*domain.Extension{},
+				Identifier:        []*domain.FHIRIdentifier{},
+				BasedOn:           []*domain.FHIRReference{},
+				Status:            "",
+				Category:          []*domain.FHIRCodeableConcept{},
+				Code:              domain.FHIRCodeableConcept{},
+				Subject: &domain.FHIRReference{
+					ID: &ID,
+				},
+				Encounter: &domain.FHIRReference{
+					ID: &ID,
+				},
+				EffectivePeriod:    &domain.FHIRPeriod{},
+				Issued:             new(string),
+				Performer:          []*domain.FHIRReference{},
+				ResultsInterpreter: []*domain.FHIRReference{},
+				Specimen:           []*domain.FHIRReference{},
+				Result:             []*domain.FHIRReference{},
+				ImagingStudy:       []*domain.FHIRReference{},
+				Media:              []*domain.FHIRDiagnosticReportMedia{},
+				Conclusion:         new(string),
+				ConclusionCode:     []*domain.FHIRCodeableConcept{},
+				PresentedForm:      []*domain.FHIRAttachment{},
+			}, nil
+		},
 	}
 }
 
@@ -2314,3 +2350,8 @@ func (fh *FHIRMock) CreateFHIRRiskAssessment(ctx context.Context, input *domain.
 func (fh *FHIRMock) GetFHIRQuestionnaire(ctx context.Context, id string) (*domain.FHIRQuestionnaireRelayPayload, error) {
 	return fh.MockGetFHIRQuestionnaireFn(ctx, id)
 }
+
+// CreateFHIRDiagnosticReport mocks the implementation of creating a diagnostic report.
+func (fh *FHIRMock) CreateFHIRDiagnosticReport(ctx context.Context, input *domain.FHIRDiagnosticReportInput) (*domain.FHIRDiagnosticReport, error) {
+	return fh.MockCreateFHIRDiagnosticReportFn(ctx, input)
+}
diff --git a/pkg/clinical/presentation/config.go b/pkg/clinical/presentation/config.go
@@ -193,6 +193,11 @@ func SetupRoutes(r *gin.Engine, cacheStore persist.CacheStore, authclient *authu
 	questionnaire.Use(rest.AuthenticationGinMiddleware(cacheStore, *authclient))
 	questionnaire.Use(rest.TenantIdentifierExtractionMiddleware(infra.FHIR))
 	questionnaire.POST("", handlers.LoadQuestionnaire)
+
+	mammography := v1.Group("/mammography")
+	mammography.Use(rest.AuthenticationGinMiddleware(cacheStore, *authclient))
+	mammography.Use(rest.TenantIdentifierExtractionMiddleware(infra.FHIR))
+	mammography.POST("", handlers.RecordMammographyResult)
 }
 
 // GQLHandler sets up a GraphQL resolver

diff --git a/pkg/clinical/presentation/rest/handlers.go b/pkg/clinical/presentation/rest/handlers.go
@@ -332,3 +332,41 @@ func (p PresentationHandlersImpl) LoadQuestionnaire(c *gin.Context) {
 
 	c.JSON(http.StatusOK, questionnaire)
 }
+
+// RecordMammographyResult is used to record mammography results
+func (p PresentationHandlersImpl) RecordMammographyResult(c *gin.Context) {
+	input := &dto.DiagnosticReportInput{
+		EncounterID: c.Request.FormValue("encounterID"),
+		Note:        c.Request.FormValue("note"),
+		Attachment:  c.Request.MultipartForm.File,
+		Findings:    c.Request.FormValue("findings"),
+	}
+
+	if err := c.Request.ParseMultipartForm(50 << 20); err != nil {
+		jsonErrorResponse(c, http.StatusBadRequest, err)
+		return
+	}
+
+	var response *dto.DiagnosticReport
+
+	for _, fileHeaders := range input.Attachment {
+		for _, fileHeader := range fileHeaders {
+			file, err := fileHeader.Open()
+			if err != nil {
+				jsonErrorResponse(c, http.StatusBadRequest, err)
+				return
+			}
+			defer file.Close()
+
+			input.File = file
+
+			response, err = p.usecases.RecordMammographyResult(c.Request.Context(), *input)
+			if err != nil {
+				jsonErrorResponse(c, http.StatusInternalServerError, err)
+				return
+			}
+		}
+	}
+
+	c.JSON(http.StatusOK, response)
+}