refactor: setup composition when starting an encounter (#402)

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

Dockerfile

@@ -1,14 +1,10 @@
 # Use the official Golang image to create a build artifact.
 # This is based on Debian and sets the GOPATH to /go.
-# https://hub.docker.com/_/golang
-FROM golang:1.21 as builder
+FROM golang:1.22-bullseye as builder
 
 # Create and change to the app directory.
 WORKDIR /app
 
-# Install wkhtmltopdf in the builder stage.
-RUN apt-get update && apt-get install -y wkhtmltopdf && apt-get clean
-
 # Copy go.sum/go.mod and warm up the module cache.
 COPY go.* ./
 RUN go mod download
@@ -22,22 +18,37 @@ COPY . .
 # Build the binary.
 RUN CGO_ENABLED=0 GOOS=linux go build -v -o server github.com/savannahghi/clinical
 
-# Use the official Alpine image for a lean production container.
-FROM alpine:3 as production
-
-# Install ca-certificates and other runtime dependencies for wkhtmltopdf.
-RUN apk add --no-cache ca-certificates
+FROM debian:bullseye-slim as production
+
+# Install necessary libraries for wkhtmltopdf.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wkhtmltopdf \
+    libstdc++6 \
+    libx11-6 \
+    libxrender1 \
+    libxext6 \
+    libfontconfig1 \
+    fonts-dejavu \
+    fonts-droid-fallback \
+    fonts-freefont-ttf \
+    fonts-liberation \
+    libqt5webkit5 \
+    libqt5widgets5 \
+    libqt5gui5 \
+    libqt5core5a \
+    libqt5network5 \
+    ca-certificates \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
 
-# Copy the wkhtmltopdf binary and related files from the builder stage to the production image.
-COPY --from=builder /usr/bin/wkhtmltopdf /usr/local/bin/
 
 # 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
+# Set the working directory to where your binary and templates are.
 WORKDIR /app
 
 # Run the web service on container startup.

pkg/clinical/application/common/defaults.go

@@ -128,8 +128,11 @@ const (
 	// LOINCExamination defines LOINC Examination note terminology code
 	LOINCExamination = "29545-1"
 
-	// LOINCPLANOFCARE defines LOINC Plan of care note terminology code
-	LOINCPLANOFCARE = "18776-5"
+	// LOINCPlanOfCare defines LOINC Plan of care note terminology code
+	LOINCPlanOfCare = "18776-5"
+
+	// LOINCProviderUnspecifiedProgressNote defines LOINC Provider unspecified progress note terminology code
+	LOINCProviderUnspecifiedProgressNote = "11506-3"
 
 	// ColposcopyCIELTerminologyCode is the terminology code for colposcopy findings
 	ColposcopyCIELTerminologyCode = "162816"

pkg/clinical/application/dto/enums.go

@@ -162,12 +162,13 @@ const (
 type CompositionCategory string
 
 const (
-	AssessmentAndPlan          CompositionCategory = "ASSESSMENT_PLAN"
-	HistoryOfPresentingIllness CompositionCategory = "HISTORY_OF_PRESENTING_ILLNESS"
-	SocialHistory              CompositionCategory = "SOCIAL_HISTORY"
-	FamilyHistory              CompositionCategory = "FAMILY_HISTORY"
-	Examination                CompositionCategory = "EXAMINATION"
-	PlanOfCare                 CompositionCategory = "PLAN_OF_CARE"
+	AssessmentAndPlan               CompositionCategory = "ASSESSMENT_PLAN"
+	HistoryOfPresentingIllness      CompositionCategory = "HISTORY_OF_PRESENTING_ILLNESS"
+	SocialHistory                   CompositionCategory = "SOCIAL_HISTORY"
+	FamilyHistory                   CompositionCategory = "FAMILY_HISTORY"
+	Examination                     CompositionCategory = "EXAMINATION"
+	PlanOfCare                      CompositionCategory = "PLAN_OF_CARE"
+	ProviderUnspecifiedProgressNote CompositionCategory = "PROGRESS_NOTE"
 )
 
 // Type enum represents type composition attribute

pkg/clinical/infrastructure/datastore/cloudhealthcare/mock/fhir_mock.go

@@ -343,6 +343,14 @@ func NewFHIRMock() *FHIRMock {
 			return &domain.FHIREncounterRelayPayload{
 				Resource: &domain.FHIREncounter{
 					ID: &resourceID,
+					Meta: &domain.FHIRMeta{
+						Source: resourceID,
+						Tag: []domain.FHIRCoding{
+							{
+								Code: (*scalarutils.Code)(&resourceID),
+							},
+						},
+					},
 				},
 			}, nil
 		},

pkg/clinical/usecases/clinical/composition.go

@@ -54,31 +54,12 @@ func (c *UseCasesClinicalImpl) CreateComposition(ctx context.Context, input dto.
 
 	id := uuid.New().String()
 
-	var compositionCategoryCode string
-
-	switch input.Category {
-	case "ASSESSMENT_PLAN":
-		compositionCategoryCode = common.LOINCAssessmentPlanCode
-	case "HISTORY_OF_PRESENTING_ILLNESS":
-		compositionCategoryCode = common.LOINCHistoryOfPresentingIllness
-	case "SOCIAL_HISTORY":
-		compositionCategoryCode = common.LOINCSocialHistory
-	case "FAMILY_HISTORY":
-		compositionCategoryCode = common.LOINCFamilyHistory
-	case "EXAMINATION":
-		compositionCategoryCode = common.LOINCExamination
-	case "PLAN_OF_CARE":
-		compositionCategoryCode = common.LOINCPLANOFCARE
-	default:
-		return nil, fmt.Errorf("category is needed")
-	}
-
-	compositionCategoryConcept, err := c.GetConcept(ctx, dto.TerminologySourceLOINC, compositionCategoryCode)
+	compositionCategoryCode, err := c.mapCategoryEnumToCode(input.Category)
 	if err != nil {
 		return nil, err
 	}
 
-	compositionTypeConcept, err := c.GetConcept(ctx, dto.TerminologySourceLOINC, common.LOINCProgressNoteCode)
+	compositionConcept, err := c.mapCompositionConcepts(ctx, compositionCategoryCode, common.LOINCProgressNoteCode)
 	if err != nil {
 		return nil, err
 	}
@@ -91,24 +72,24 @@ func (c *UseCasesClinicalImpl) CreateComposition(ctx context.Context, input dto.
 		Type: &domain.FHIRCodeableConceptInput{
 			Coding: []*domain.FHIRCodingInput{
 				{
-					System:  (*scalarutils.URI)(&compositionTypeConcept.URL),
-					Code:    scalarutils.Code(compositionTypeConcept.ID),
-					Display: compositionTypeConcept.DisplayName,
+					System:  (*scalarutils.URI)(&compositionConcept.CompositionTypeConcept.URL),
+					Code:    scalarutils.Code(compositionConcept.CompositionTypeConcept.ID),
+					Display: compositionConcept.CompositionTypeConcept.DisplayName,
 				},
 			},
-			Text: compositionTypeConcept.DisplayName,
+			Text: compositionConcept.CompositionTypeConcept.DisplayName,
 		},
 		Category: []*domain.FHIRCodeableConceptInput{
 			{
 				ID: &id,
 				Coding: []*domain.FHIRCodingInput{
 					{
-						System:  (*scalarutils.URI)(&compositionCategoryConcept.URL),
-						Code:    scalarutils.Code(compositionCategoryConcept.ID),
-						Display: compositionCategoryConcept.DisplayName,
+						System:  (*scalarutils.URI)(&compositionConcept.CompositionCategoryConcept.URL),
+						Code:    scalarutils.Code(compositionConcept.CompositionCategoryConcept.ID),
+						Display: compositionConcept.CompositionCategoryConcept.DisplayName,
 					},
 				},
-				Text: compositionCategoryConcept.DisplayName,
+				Text: compositionConcept.CompositionCategoryConcept.DisplayName,
 			},
 		},
 		Subject: &domain.FHIRReferenceInput{
@@ -132,18 +113,18 @@ func (c *UseCasesClinicalImpl) CreateComposition(ctx context.Context, input dto.
 		Section: []*domain.FHIRCompositionSectionInput{
 			{
 				ID:    &id,
-				Title: &compositionCategoryConcept.DisplayName,
+				Title: &compositionConcept.CompositionCategoryConcept.DisplayName,
 				Code: &domain.FHIRCodeableConceptInput{
 					ID: &id,
 					Coding: []*domain.FHIRCodingInput{
 						{
 							ID:      &id,
-							System:  (*scalarutils.URI)(&compositionCategoryConcept.URL),
-							Code:    scalarutils.Code(compositionCategoryConcept.ID),
-							Display: compositionCategoryConcept.DisplayName,
+							System:  (*scalarutils.URI)(&compositionConcept.CompositionCategoryConcept.URL),
+							Code:    scalarutils.Code(compositionConcept.CompositionCategoryConcept.ID),
+							Display: compositionConcept.CompositionCategoryConcept.DisplayName,
 						},
 					},
-					Text: compositionTypeConcept.DisplayName,
+					Text: compositionConcept.CompositionTypeConcept.DisplayName,
 				},
 				Author: []*domain.FHIRReferenceInput{
 					{
@@ -178,12 +159,12 @@ func (c *UseCasesClinicalImpl) CreateComposition(ctx context.Context, input dto.
 			ID: &id,
 			Coding: []*domain.FHIRCodingInput{
 				{
-					System:  (*scalarutils.URI)(&compositionCategoryConcept.URL),
-					Code:    scalarutils.Code(compositionCategoryConcept.ID),
-					Display: compositionCategoryConcept.DisplayName,
+					System:  (*scalarutils.URI)(&compositionConcept.CompositionCategoryConcept.URL),
+					Code:    scalarutils.Code(compositionConcept.CompositionCategoryConcept.ID),
+					Display: compositionConcept.CompositionCategoryConcept.DisplayName,
 				},
 			},
-			Text: compositionCategoryConcept.DisplayName,
+			Text: compositionConcept.CompositionCategoryConcept.DisplayName,
 		},
 	}
 
@@ -332,21 +313,9 @@ func (c *UseCasesClinicalImpl) AppendNoteToComposition(ctx context.Context, id s
 
 	organizationRef := fmt.Sprintf("Organization/%s", identifiers.OrganizationID)
 
-	var compositionCategoryCode string
-
-	switch input.Category {
-	case "ASSESSMENT_PLAN":
-		compositionCategoryCode = common.LOINCAssessmentPlanCode
-	case "HISTORY_OF_PRESENTING_ILLNESS":
-		compositionCategoryCode = common.LOINCHistoryOfPresentingIllness
-	case "SOCIAL_HISTORY":
-		compositionCategoryCode = common.LOINCSocialHistory
-	case "FAMILY_HISTORY":
-		compositionCategoryCode = common.LOINCFamilyHistory
-	case "EXAMINATION":
-		compositionCategoryCode = common.LOINCExamination
-	case "PLAN_OF_CARE":
-		compositionCategoryCode = common.LOINCPLANOFCARE
+	compositionCategoryCode, err := c.mapCategoryEnumToCode(input.Category)
+	if err != nil {
+		return nil, err
 	}
 
 	compositionCategoryConcept, err := c.GetConcept(ctx, dto.TerminologySourceLOINC, compositionCategoryCode)

pkg/clinical/usecases/clinical/composition_helpers.go

@@ -0,0 +1,60 @@
+package clinical
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/savannahghi/clinical/pkg/clinical/application/common"
+	"github.com/savannahghi/clinical/pkg/clinical/application/dto"
+	"github.com/savannahghi/clinical/pkg/clinical/domain"
+)
+
+// CompositionConcept is used to map composition concepts
+type CompositionConcept struct {
+	CompositionCategoryConcept *domain.Concept
+	CompositionTypeConcept     *domain.Concept
+}
+
+// mapCompositionConcepts composes a unified representation of composition concepts and types into a single model
+func (c *UseCasesClinicalImpl) mapCompositionConcepts(ctx context.Context, compositionCategoryCode, conceptID string) (*CompositionConcept, error) {
+	compositionCategoryConcept, err := c.GetConcept(ctx, dto.TerminologySourceLOINC, compositionCategoryCode)
+	if err != nil {
+		return nil, err
+	}
+
+	compositionTypeConcept, err := c.GetConcept(ctx, dto.TerminologySourceLOINC, conceptID)
+	if err != nil {
+		return nil, err
+	}
+
+	return &CompositionConcept{
+		CompositionCategoryConcept: compositionCategoryConcept,
+		CompositionTypeConcept:     compositionTypeConcept,
+	}, nil
+}
+
+// mapCategoryEnumToCode is used to map various composition categories to respective LOINC codes
+func (*UseCasesClinicalImpl) mapCategoryEnumToCode(category dto.CompositionCategory) (string, error) {
+	var compositionCategoryCode string
+
+	switch category {
+	case "ASSESSMENT_PLAN":
+		compositionCategoryCode = common.LOINCAssessmentPlanCode
+	case "HISTORY_OF_PRESENTING_ILLNESS":
+		compositionCategoryCode = common.LOINCHistoryOfPresentingIllness
+	case "SOCIAL_HISTORY":
+		compositionCategoryCode = common.LOINCSocialHistory
+	case "FAMILY_HISTORY":
+		compositionCategoryCode = common.LOINCFamilyHistory
+	case "EXAMINATION":
+		compositionCategoryCode = common.LOINCExamination
+	case "PLAN_OF_CARE":
+		compositionCategoryCode = common.LOINCPlanOfCare
+	case "PROGRESS_NOTE":
+		compositionCategoryCode = common.LOINCProviderUnspecifiedProgressNote
+	default:
+		return "", fmt.Errorf("category is needed")
+	}
+
+	return compositionCategoryCode, nil
+}