feat: record biopsy (#354)

- biopsy is recorded as diagnostic report as recommended by FHIR

[Link to documentation]: https://savannahghi.atlassian.net/wiki/spaces/OHE/pages/468025506/API+Documentation#Record-Biopsy

Signed-off-by: Kathurima Kimathi <kathurimakimathi415@gmail.com>

.golangci.yaml

@@ -27,7 +27,6 @@ linters:
     - ireturn
     - importas
     - wsl
-    - revive
     - exportloopref
     - nilerr
     - makezero
@@ -39,4 +38,11 @@ linters-settings:
   funlen:
     lines: -1 
     statements: -1
+  revive:
+    rules:
+      - name: unused-parameter
+        severity: warning
+        disabled: true
+        arguments:
+          - allowRegex: "^_"
 

pkg/clinical/application/common/defaults.go

@@ -155,14 +155,17 @@ const (
 	// LowRiskCIELCode represents the CIEL code for a low-risk condition
 	LowRiskCIELCode = "166675"
 
-	// CIELTerminologySystem is the identity of ciel terminology system
+	// 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"
+
+	// BiopsyTerminologySystem is the terminology code used to represent Biopsy of cervix.
+	BiopsyTerminologySystem = "161826"
 )
 
 // DefaultIdentifier assigns a patient a code to function as their

pkg/clinical/application/dto/input.go

@@ -228,7 +228,7 @@ type Expression struct {
 type DiagnosticReportInput struct {
 	EncounterID string `json:"encounterID,omitempty"  validate:"required"`
 	Note        string `json:"note,omitempty"`
-	Media       Media  `json:"media"  validate:"required"`
+	Media       *Media `json:"media"`
 	Findings    string `json:"findings,omitempty" validate:"required"`
 }
 

pkg/clinical/presentation/config.go

@@ -49,6 +49,8 @@ var ClinicalAllowedOrigins = []string{
 	"https://review-advantage.web.app",
 	"https://prod-empower.web.app",
 	"https://staging-empower.web.app",
+	"https://uat.empower.savannahghi.org",
+	"https://empower.savannahghi.org",
 }
 
 var (

pkg/clinical/presentation/graph/clinical.graphql

@@ -218,4 +218,5 @@ extend type Mutation {
 
   # Diagnostic Report
   recordMammographyResult(input: DiagnosticReportInput!): DiagnosticReport!
+  recordBiopsy(input: DiagnosticReportInput!): DiagnosticReport!
 }

pkg/clinical/usecases/clinical/diagnostic_report.go

@@ -32,11 +32,39 @@ func (c *UseCasesClinicalImpl) RecordMammographyResult(ctx context.Context, inpu
 		return nil, err
 	}
 
-	observationsReference := fmt.Sprintf("Observation/%s", observationOutput.ID)
+	return c.RecordDiagnosticReport(ctx, common.MammogramTerminologyCode, input, observationOutput, nil)
+}
+
+// RecordBiopsy is used to record biopsy test results as observations
+// FHIR recommends use of diagnostic resource to record the findings and interpretation of biopsy test results
+// performed on patients, groups of patients, devices, and locations, and/or specimens.
+func (c *UseCasesClinicalImpl) RecordBiopsy(ctx context.Context, input dto.DiagnosticReportInput) (*dto.DiagnosticReport, error) {
+	err := input.Validate()
+	if err != nil {
+		return nil, err
+	}
+
+	observationInput := &dto.ObservationInput{
+		Status:      dto.ObservationStatusFinal,
+		EncounterID: input.EncounterID,
+		Value:       input.Findings,
+	}
+
+	observationOutput, err := c.RecordObservation(ctx, *observationInput, common.BiopsyTerminologySystem, []ObservationInputMutatorFunc{addProcedureCategory})
+	if err != nil {
+		return nil, err
+	}
+
+	return c.RecordDiagnosticReport(ctx, common.BiopsyTerminologySystem, input, observationOutput, []DiagnosticReportMutatorFunc{addCytologyCategory})
+}
+
+// RecordDiagnosticReport is a re-usable method to help with diagnostic report recording
+func (c *UseCasesClinicalImpl) RecordDiagnosticReport(ctx context.Context, conceptID string, input dto.DiagnosticReportInput, observation *dto.Observation, mutators []DiagnosticReportMutatorFunc) (*dto.DiagnosticReport, error) {
+	observationsReference := fmt.Sprintf("Observation/%s", observation.ID)
 	observationType := scalarutils.URI("Observation")
-	encounterReference := fmt.Sprintf("Encounter/%s", observationOutput.EncounterID)
+	encounterReference := fmt.Sprintf("Encounter/%s", observation.EncounterID)
 	encounterType := scalarutils.URI("Encounter")
-	patientReference := fmt.Sprintf("Patient/%s", observationOutput.PatientID)
+	patientReference := fmt.Sprintf("Patient/%s", observation.PatientID)
 	patientType := scalarutils.URI("Patient")
 
 	tags, err := c.GetTenantMetaTags(ctx)
@@ -57,18 +85,17 @@ func (c *UseCasesClinicalImpl) RecordMammographyResult(ctx context.Context, inpu
 	orgRef := fmt.Sprintf("Organization/%s", *facility.Resource.ID)
 	orgType := scalarutils.URI("Organization")
 	id := uuid.New().String()
-	mediaReference := fmt.Sprintf("Media/%s", input.Media.ID)
-	mediaType := scalarutils.URI("Media")
 	instant := scalarutils.Instant(time.Now().Format(time.RFC3339))
 
-	concept, err := c.GetConcept(ctx, dto.TerminologySourceCIEL, common.MammogramTerminologyCode)
+	concept, err := c.GetConcept(ctx, dto.TerminologySourceCIEL, conceptID)
 	if err != nil {
 		return nil, err
 	}
 
 	diagnosticReport := &domain.FHIRDiagnosticReportInput{
-		ID:     &id,
-		Status: domain.DiagnosticReportStatusPreliminary,
+		ID:       &id,
+		Status:   domain.DiagnosticReportStatusFinal,
+		Category: []*domain.FHIRCodeableConceptInput{},
 		Code: domain.FHIRCodeableConceptInput{
 			Coding: []*domain.FHIRCodingInput{
 				{
@@ -80,12 +107,12 @@ func (c *UseCasesClinicalImpl) RecordMammographyResult(ctx context.Context, inpu
 			Text: concept.DisplayName,
 		},
 		Subject: &domain.FHIRReferenceInput{
-			ID:        &observationOutput.PatientID,
+			ID:        &observation.PatientID,
 			Reference: &patientReference,
 			Type:      &patientType,
 		},
 		Encounter: &domain.FHIRReferenceInput{
-			ID:        &observationOutput.EncounterID,
+			ID:        &observation.EncounterID,
 			Reference: &encounterReference,
 			Type:      &encounterType,
 		},
@@ -106,19 +133,10 @@ func (c *UseCasesClinicalImpl) RecordMammographyResult(ctx context.Context, inpu
 				Display:   *facility.Resource.Name,
 			},
 		},
-		Media: []*domain.FHIRDiagnosticReportMediaInput{
-			{
-				ID: &input.Media.ID,
-				Link: &domain.FHIRReferenceInput{
-					Reference: &mediaReference,
-					Type:      &mediaType,
-				},
-			},
-		},
 		Conclusion: &input.Note,
 		Result: []*domain.FHIRReferenceInput{
 			{
-				ID:        &observationOutput.ID,
+				ID:        &observation.ID,
 				Reference: &observationsReference,
 				Type:      &observationType,
 			},
@@ -129,6 +147,30 @@ func (c *UseCasesClinicalImpl) RecordMammographyResult(ctx context.Context, inpu
 		Tag: tags,
 	}
 
+	if input.Media != nil {
+		mediaReference := fmt.Sprintf("Media/%s", input.Media.ID)
+		mediaType := scalarutils.URI("Media")
+
+		diagnosticReport.Media = []*domain.FHIRDiagnosticReportMediaInput{
+			{
+				ID: &input.Media.ID,
+				Link: &domain.FHIRReferenceInput{
+					Reference: &mediaReference,
+					Type:      &mediaType,
+				},
+			},
+		}
+	}
+
+	if len(mutators) > 0 {
+		for _, mutator := range mutators {
+			err = mutator(ctx, diagnosticReport)
+			if err != nil {
+				return nil, err
+			}
+		}
+	}
+
 	result, err := c.infrastructure.FHIR.CreateFHIRDiagnosticReport(ctx, diagnosticReport)
 	if err != nil {
 		return nil, err