feat: append notes to composition section

- adds appending various notes to the composition section

gqlgen.yml

@@ -42,7 +42,6 @@ models:
   PatchPatientInput:
     model:
       - github.com/savannahghi/clinical/pkg/clinical/application/dto.PatientInput
-
   Date:
     model:
       - "github.com/savannahghi/scalarutils.Date"

pkg/clinical/application/common/defaults.go

@@ -112,6 +112,21 @@ const (
 
 	// LOINCAssessmentPlanCode defines LOINC assessment plan note terminology code
 	LOINCAssessmentPlanCode = "51847-2"
+
+	// LOINCHistoryOfPresentingIllness defines LOINC history of presenting illness note terminology code
+	LOINCHistoryOfPresentingIllness = "10164-2"
+
+	// LOINCSocialHistory defines LOINC social history note terminology code
+	LOINCSocialHistory = "29762-2"
+
+	// LOINCFamilyHistory defines LOINC family history note terminology code
+	LOINCFamilyHistory = "10157-6"
+
+	// LOINCExamination defines LOINC Examination note terminology code
+	LOINCExamination = "29545-1"
+
+	// LOINCPLANOFCARE defines LOINC Plan of care note terminology code
+	LOINCPLANOFCARE = "18776-5"
 )
 
 // DefaultIdentifier assigns a patient a code to function as their

pkg/clinical/application/dto/composition_output.go

@@ -15,6 +15,7 @@ type Composition struct {
 	EncounterID string                `json:"encounterID,omitempty"`
 	Date        *scalarutils.Date     `json:"date"`
 	Author      string                `json:"author,omitempty"`
+	Section     []*Section            `json:"section"`
 }
 
 // CompositionEdge is a composition edge

pkg/clinical/application/dto/enums.go

@@ -146,7 +146,12 @@ const (
 type CompositionCategory string
 
 const (
-	AssessmentAndPlan CompositionCategory = "ASSESSMENT_PLAN"
+	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"
 )
 
 // Type enum represents type composition attribute

pkg/clinical/application/dto/input.go

@@ -110,3 +110,22 @@ type CompositionInput struct {
 	Status      CompositionStatusEnum `json:"status"`
 	Note        string                `json:"note"`
 }
+
+// PatchCompositionInput models the patch composition input
+type PatchCompositionInput struct {
+	Type     CompositionType       `json:"type"`
+	Category CompositionCategory   `json:"category"`
+	Status   CompositionStatusEnum `json:"status"`
+	Note     string                `json:"note"`
+	Section  []*SectionInput       `json:"section"`
+}
+
+// SectionInput models the composition section input
+type SectionInput struct {
+	ID      string          `json:"id,omitempty"`
+	Title   string          `json:"title"`
+	Code    string          `json:"code"`
+	Author  string          `json:"author"`
+	Text    string          `json:"text"`
+	Section []*SectionInput `json:"section"`
+}

pkg/clinical/application/dto/output.go

@@ -145,3 +145,13 @@ func CreateMediaConnection(mediaList []*Media, pageInfo PageInfo, total int) Med
 
 	return connection
 }
+
+// Section defines a composition section output model
+type Section struct {
+	ID      *string    `json:"id,omitempty"`
+	Title   *string    `json:"title,omitempty"`
+	Code    *string    `json:"code,omitempty"`
+	Author  *string    `json:"author,omitempty"`
+	Text    string     `json:"text,omitempty"`
+	Section []*Section `json:"section,omitempty"`
+}

pkg/clinical/domain/composition.go

@@ -178,7 +178,7 @@ type FHIRCompositionInput struct {
 	Section []*FHIRCompositionSectionInput `json:"section,omitempty"`
 
 	// Meta stores more information about the resource
-	Meta FHIRMetaInput `json:"meta,omitempty"`
+	Meta *FHIRMetaInput `json:"meta,omitempty"`
 
 	// Extension is an optional element that provides additional information not captured in the basic resource definition
 	Extension []*FHIRExtension `json:"extension,omitempty"`

pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir.go

@@ -865,7 +865,7 @@ func (fh StoreImpl) CreateFHIRComposition(_ context.Context, input domain.FHIRCo
 
 // UpdateFHIRComposition updates a FHIRComposition instance
 // The resource must have its ID set.
-func (fh StoreImpl) UpdateFHIRComposition(_ context.Context, input domain.FHIRCompositionInput) (*domain.FHIRCompositionRelayPayload, error) {
+func (fh StoreImpl) UpdateFHIRComposition(_ context.Context, input domain.FHIRCompositionInput) (*domain.FHIRComposition, error) {
 	if input.ID == nil {
 		return nil, fmt.Errorf("can't update with a nil ID")
 	}
@@ -882,11 +882,7 @@ func (fh StoreImpl) UpdateFHIRComposition(_ context.Context, input domain.FHIRCo
 		return nil, fmt.Errorf("unable to create/update %s resource: %w", compositionResourceType, err)
 	}
 
-	output := &domain.FHIRCompositionRelayPayload{
-		Resource: resource,
-	}
-
-	return output, nil
+	return resource, nil
 }
 
 // DeleteFHIRComposition deletes the FHIRComposition identified by the supplied ID
@@ -1620,3 +1616,36 @@ func (fh StoreImpl) SearchFHIRPatient(_ context.Context, searchParams string, te
 
 	return &output, nil
 }
+
+// GetFHIRComposition retrieves instances of FHIRComposition by ID
+func (fh StoreImpl) GetFHIRComposition(_ context.Context, id string) (*domain.FHIRCompositionRelayPayload, error) {
+	resource := &domain.FHIRComposition{}
+
+	err := fh.Dataset.GetFHIRResource(compositionResourceType, id, resource)
+	if err != nil {
+		return nil, fmt.Errorf("unable to get %s with ID %s, err: %w", compositionResourceType, id, err)
+	}
+
+	payload := &domain.FHIRCompositionRelayPayload{
+		Resource: resource,
+	}
+
+	return payload, nil
+}
+
+// PatchFHIRComposition is used to patch a composition resource
+func (fh StoreImpl) PatchFHIRComposition(_ context.Context, id string, input domain.FHIRCompositionInput) (*domain.FHIRComposition, error) {
+	payload, err := converterandformatter.StructToMap(input)
+	if err != nil {
+		return nil, fmt.Errorf("unable to turn %s input into a map: %w", compositionResourceType, err)
+	}
+
+	resource := &domain.FHIRComposition{}
+
+	err = fh.Dataset.PatchFHIRResource(compositionResourceType, id, payload, resource)
+	if err != nil {
+		return nil, fmt.Errorf("unable to patch %s resource: %w", compositionResourceType, err)
+	}
+
+	return resource, nil
+}

pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir_unit_test.go

@@ -2189,6 +2189,57 @@ func TestStoreImpl_CreateFHIRComposition(t *testing.T) {
 		})
 	}
 }
+func TestStoreImpl_GetFHIRComposition(t *testing.T) {
+
+	type args struct {
+		ctx context.Context
+		id  string
+	}
+	tests := []struct {
+		name    string
+		args    args
+		wantErr bool
+	}{
+		{
+			name: "happy case: get composition",
+			args: args{
+				ctx: context.Background(),
+				id:  uuid.NewString(),
+			},
+			wantErr: false,
+		},
+		{
+			name: "sad case: error retrieving fhir resource",
+			args: args{
+				ctx: context.Background(),
+				id:  uuid.NewString(),
+			},
+			wantErr: true,
+		},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dataset := fakeDataset.NewFakeFHIRRepositoryMock()
+			fh := FHIR.NewFHIRStoreImpl(dataset)
+
+			if tt.name == "sad case: error retrieving fhir resource" {
+				dataset.MockGetFHIRResourceFn = func(resourceType, fhirResourceID string, resource interface{}) error {
+					return fmt.Errorf("an error occurred")
+				}
+			}
+
+			got, err := fh.GetFHIRComposition(tt.args.ctx, tt.args.id)
+			if (err != nil) != tt.wantErr {
+				t.Errorf("StoreImpl.GetFHIRComposition() error = %v, wantErr %v", err, tt.wantErr)
+				return
+			}
+			if !tt.wantErr && got == nil {
+				t.Errorf("expected a response but got: %v", got)
+				return
+			}
+		})
+	}
+}
 
 func TestStoreImpl_UpdateFHIRComposition(t *testing.T) {