release: staging to production (#296)

* add conditions to patient timeline (#276) * fix: fix listing of patient conditions (#278) * fix: check encounter finished status when creating allergies (#279) * feat: add record blood sugar api (#280) * feat: add api to fetch a patient's blood sugar observation (#281) * add last menstrual period vital (#283) * add diastolic blood pressure observation (#284) * adds fetching patient's diastolic blood pressure (#286) * feat: token caching (#287) * feat: add composition resource (#282) * list patient's compositions (#289) * query observations with encounterID filter (#290) * query observations with encounterID filter * updates * query conditions with encounterID (#291) * query compositions with encounterID (#292) * feat: add date filter query on observations (#293) - rebased - has observations date filter changes ONLY * feat: add date filter on conditions (#294) - adds date filter as a search param for conditions --------- Co-authored-by: EspiraMarvin <[email protected]> Co-authored-by: Salaton <[email protected]> Co-authored-by: Charles Muchogo <[email protected]>
savannahghi · Dec 14, 2023 · 582f29e · 582f29e
1 parent f093351
commit 582f29e
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Showing 37 changed files with 5,970 additions and 872 deletions.
diff --git a/go.mod b/go.mod
@@ -10,6 +10,7 @@ require (
 	github.com/ahmetb/go-linq/v3 v3.2.0
 	github.com/asaskevich/govalidator v0.0.0-20230301143203-a9d515a09cc2
 	github.com/brianvoe/gofakeit v3.18.0+incompatible
+	github.com/chenyahui/gin-cache v1.8.1
 	github.com/getsentry/sentry-go v0.23.0
 	github.com/gin-contrib/cors v1.4.0
 	github.com/gin-gonic/gin v1.9.1
@@ -52,20 +53,23 @@ require (
 	firebase.google.com/go v3.13.0+incompatible // indirect
 	github.com/agnivade/levenshtein v1.1.1 // indirect
 	github.com/aws/aws-sdk-go v1.44.328 // indirect
-	github.com/bytedance/sonic v1.10.0 // indirect
+	github.com/bytedance/sonic v1.10.1 // indirect
 	github.com/census-instrumentation/opencensus-proto v0.4.1 // indirect
+	github.com/cespare/xxhash/v2 v2.2.0 // indirect
 	github.com/chenzhuoyu/base64x v0.0.0-20230717121745-296ad89f973d // indirect
 	github.com/chenzhuoyu/iasm v0.9.0 // indirect
 	github.com/cpuguy83/go-md2man/v2 v2.0.2 // indirect
 	github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc // indirect
+	github.com/dgryski/go-rendezvous v0.0.0-20200823014737-9f7001d12a5f // indirect
 	github.com/felixge/httpsnoop v1.0.3 // indirect
 	github.com/gabriel-vasile/mimetype v1.4.2 // indirect
 	github.com/gin-contrib/sse v0.1.0 // indirect
 	github.com/go-logr/logr v1.2.4 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
 	github.com/go-playground/locales v0.14.1 // indirect
 	github.com/go-playground/universal-translator v0.18.1 // indirect
-	github.com/go-playground/validator/v10 v10.15.1 // indirect
+	github.com/go-playground/validator/v10 v10.15.5 // indirect
+	github.com/go-redis/redis/v8 v8.11.5 // indirect
 	github.com/goccy/go-json v0.10.2 // indirect
 	github.com/gofrs/uuid v4.4.0+incompatible // indirect
 	github.com/golang-jwt/jwt v3.2.2+incompatible // indirect
@@ -79,6 +83,7 @@ require (
 	github.com/gorilla/websocket v1.5.0 // indirect
 	github.com/hashicorp/golang-lru/v2 v2.0.5 // indirect
 	github.com/imroc/req v0.3.2 // indirect
+	github.com/jellydator/ttlcache/v2 v2.11.1 // indirect
 	github.com/jmespath/go-jmespath v0.4.0 // indirect
 	github.com/json-iterator/go v1.1.12 // indirect
 	github.com/klauspost/cpuid/v2 v2.2.5 // indirect
@@ -87,7 +92,7 @@ require (
 	github.com/mattn/go-isatty v0.0.19 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
 	github.com/modern-go/reflect2 v1.0.2 // indirect
-	github.com/pelletier/go-toml/v2 v2.0.9 // indirect
+	github.com/pelletier/go-toml/v2 v2.1.0 // indirect
 	github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
 	github.com/prometheus/prometheus v0.46.0 // indirect
 	github.com/russross/blackfriday/v2 v2.1.0 // indirect
@@ -109,13 +114,13 @@ require (
 	go.opentelemetry.io/otel/metric v1.16.0 // indirect
 	go.opentelemetry.io/otel/sdk v1.16.0 // indirect
 	go.opentelemetry.io/otel/trace v1.16.0 // indirect
-	golang.org/x/arch v0.4.0 // indirect
-	golang.org/x/crypto v0.12.0 // indirect
+	golang.org/x/arch v0.5.0 // indirect
+	golang.org/x/crypto v0.14.0 // indirect
 	golang.org/x/mod v0.12.0 // indirect
-	golang.org/x/net v0.14.0 // indirect
-	golang.org/x/sync v0.3.0 // indirect
-	golang.org/x/sys v0.11.0 // indirect
-	golang.org/x/text v0.12.0 // indirect
+	golang.org/x/net v0.16.0 // indirect
+	golang.org/x/sync v0.4.0 // indirect
+	golang.org/x/sys v0.13.0 // indirect
+	golang.org/x/text v0.13.0 // indirect
 	golang.org/x/time v0.3.0 // indirect
 	golang.org/x/tools v0.12.0 // indirect
 	golang.org/x/xerrors v0.0.0-20220907171357-04be3eba64a2 // indirect

diff --git a/go.sum b/go.sum
diff --git a/pkg/clinical/application/common/defaults.go b/pkg/clinical/application/common/defaults.go
@@ -56,6 +56,15 @@ const (
 	// MuacCIELTerminologyCode is the terminology code for mid-upper arm circumference
 	MuacCIELTerminologyCode = "1343"
 
+	// BloodSugarCIELTerminologyCode is the terminology code for blood sugar (Serum glucose)
+	BloodSugarCIELTerminologyCode = "887"
+
+	// DiastolicBloodPressureTerminologyCode is the terminology code for diastolic blood pressure
+	DiastolicBloodPressureCIELTerminologyCode = "5086"
+
+	// LastMenstrualPeriodCIELTerminologyCode is the terminology code for last menstrual period
+	LastMenstrualPeriodCIELTerminologyCode = "1427"
+
 	// Spoc2CIELTerminologyCode is the terminology code oxygen saturation
 	OxygenSaturationCIELTerminologyCode = "5092"
 
@@ -97,6 +106,12 @@ const (
 
 	// AddFHIRIDToProgram is the topic where details to update a program's fhir ID will be published to
 	AddFHIRIDToProgram = "program.fhirid.update"
+
+	// LOINCProgressNoteCode defines LOINC progress note terminology code
+	LOINCProgressNoteCode = "81216-4"
+
+	// LOINCAssessmentPlanCode defines LOINC assessment plan note terminology code
+	LOINCAssessmentPlanCode = "51847-2"
 )
 
 // DefaultIdentifier assigns a patient a code to function as their

diff --git a/pkg/clinical/application/dto/allergy_output.go b/pkg/clinical/application/dto/allergy_output.go
@@ -36,7 +36,7 @@ type AllergyConnection struct {
 	PageInfo   PageInfo
 }
 
-// CreateConditionConnection creates a connection that follows the GraphQl Cursor Connection Specification
+// CreateAllergyConnection creates a connection that follows the GraphQl Cursor Connection Specification
 func CreateAllergyConnection(allergies []*Allergy, pageInfo PageInfo, total int) AllergyConnection {
 	connection := AllergyConnection{
 		TotalCount: total,

diff --git a/pkg/clinical/application/dto/composition_output.go b/pkg/clinical/application/dto/composition_output.go
@@ -0,0 +1,51 @@
+package dto
+
+import (
+	"github.com/savannahghi/scalarutils"
+)
+
+// Composition is a minimal representation of a fhir Composition
+type Composition struct {
+	ID          string                `json:"id,omitempty"`
+	Text        string                `json:"text,omitempty"`
+	Type        CompositionType       `json:"type,omitempty"`
+	Category    CompositionCategory   `json:"category,omitempty"`
+	Status      CompositionStatusEnum `json:"status,omitempty"`
+	PatientID   string                `json:"patientID,omitempty"`
+	EncounterID string                `json:"encounterID,omitempty"`
+	Date        *scalarutils.Date     `json:"date"`
+	Author      string                `json:"author,omitempty"`
+}
+
+// CompositionEdge is a composition edge
+type CompositionEdge struct {
+	Node   Composition
+	Cursor string
+}
+
+// CompositionConnection  is a Composition Connection Type
+type CompositionConnection struct {
+	TotalCount int
+	Edges      []CompositionEdge
+	PageInfo   PageInfo
+}
+
+// CreateCompositionConnection creates a connection that follows the GraphQl Cursor Connection Specification
+func CreateCompositionConnection(compositions []Composition, pageInfo PageInfo, total int) CompositionConnection {
+	connection := CompositionConnection{
+		TotalCount: total,
+		Edges:      []CompositionEdge{},
+		PageInfo:   pageInfo,
+	}
+
+	for _, composition := range compositions {
+		edge := CompositionEdge{
+			Node:   composition,
+			Cursor: composition.ID,
+		}
+
+		connection.Edges = append(connection.Edges, edge)
+	}
+
+	return connection
+}
diff --git a/pkg/clinical/application/dto/condition_output.go b/pkg/clinical/application/dto/condition_output.go
@@ -13,7 +13,7 @@ type Condition struct {
 	Category ConditionCategory `json:"category"`
 
 	OnsetDate    *scalarutils.Date `json:"onsetDate"`
-	RecordedDate scalarutils.Date  `json:"recordedDate"`
+	RecordedDate *scalarutils.Date `json:"recordedDate"`
 
 	Note string `json:"note"`
 

diff --git a/pkg/clinical/application/dto/enums.go b/pkg/clinical/application/dto/enums.go
@@ -116,7 +116,7 @@ const (
 	ConditionStatusUnknown  ConditionStatus = "UNKNOWN"
 )
 
-// ConditionStatus represents status of a FHIR condition
+// ConditionCategory represents status of a FHIR condition
 type ConditionCategory string
 
 const (
@@ -133,3 +133,35 @@ const (
 	TerminologySourceSNOMEDCT TerminologySource = "SNOMED_CT"
 	TerminologySourceLOINC    TerminologySource = "LOINC"
 )
+
+// LOINCCodes represents LOINC assessment codes
+type LOINCCodes string
+
+const (
+	LOINCPlanOfCareCode     LOINCCodes = "18776-5"
+	LOINCAssessmentPlanCode LOINCCodes = "51847-2"
+)
+
+// CompositionCategory enum represents category composition attribute
+type CompositionCategory string
+
+const (
+	AssessmentAndPlan CompositionCategory = "ASSESSMENT_PLAN"
+)
+
+// Type enum represents type composition attribute
+type CompositionType string
+
+const (
+	ProgressNote CompositionType = "PROGRESS_NOTE"
+)
+
+// CompositionStatus enum represents status composition attribute
+type CompositionStatusEnum string
+
+const (
+	CompositionStatuEnumPreliminary               CompositionStatusEnum = "PRELIMINARY"
+	CompositionStatuEnumFinal                     CompositionStatusEnum = "FINAL"
+	CompositionStatuEnumAmended                   CompositionStatusEnum = "AMENDED"
+	CompositionStatuEnumEnteredInErrorPreliminary CompositionStatusEnum = "ENTERED_IN_ERROR"
+)
diff --git a/pkg/clinical/application/dto/input.go b/pkg/clinical/application/dto/input.go
@@ -101,3 +101,12 @@ type MediaInput struct {
 	EncounterID string                             `json:"encounterID"`
 	File        map[string][]*multipart.FileHeader `form:"file" json:"file"`
 }
+
+// CompositionInput models the composition input
+type CompositionInput struct {
+	EncounterID string                `json:"encounterID"`
+	Type        CompositionType       `json:"type"`
+	Category    CompositionCategory   `json:"category"`
+	Status      CompositionStatusEnum `json:"status"`
+	Note        string                `json:"note"`
+}
diff --git a/pkg/clinical/application/dto/observation_output.go b/pkg/clinical/application/dto/observation_output.go
@@ -24,7 +24,7 @@ type ObservationConnection struct {
 	PageInfo   PageInfo
 }
 
-// CreateConditionConnection creates a connection that follows the GraphQl Cursor Connection Specification
+// CreateObservationConnection creates a connection that follows the GraphQl Cursor Connection Specification
 func CreateObservationConnection(observations []*Observation, pageInfo PageInfo, total int) ObservationConnection {
 	connection := ObservationConnection{
 		TotalCount: total,

diff --git a/pkg/clinical/domain/complex_types.go b/pkg/clinical/domain/complex_types.go
@@ -2099,6 +2099,7 @@ type CompositionStatusEnum string
 const (
 	// CompositionStatusEnumPreliminary ...
 	CompositionStatusEnumPreliminary CompositionStatusEnum = "preliminary"
+	CompositionStatusEnumRegistered  CompositionStatusEnum = "registered"
 	// CompositionStatusEnumFinal ...
 	CompositionStatusEnumFinal CompositionStatusEnum = "final"
 	// CompositionStatusEnumAmended ...

diff --git a/pkg/clinical/domain/composition.go b/pkg/clinical/domain/composition.go
@@ -223,7 +223,7 @@ type FHIRCompositionSection struct {
 	Title *string `json:"title,omitempty"`
 
 	// A code identifying the kind of content contained within the section. This must be consistent with the section title.
-	Code *scalarutils.Code `json:"code,omitempty"`
+	Code *FHIRCodeableConceptInput `json:"code,omitempty"`
 
 	// Identifies who is responsible for the information in this section, not necessarily who typed it in.
 	Author []*FHIRReference `json:"author,omitempty"`
@@ -259,7 +259,7 @@ type FHIRCompositionSectionInput struct {
 	Title *string `json:"title,omitempty"`
 
 	// A code identifying the kind of content contained within the section. This must be consistent with the section title.
-	Code *scalarutils.Code `json:"code,omitempty"`
+	Code *FHIRCodeableConceptInput `json:"code,omitempty"`
 
 	// Identifies who is responsible for the information in this section, not necessarily who typed it in.
 	Author []*FHIRReferenceInput `json:"author,omitempty"`
@@ -300,6 +300,16 @@ type FHIRCompositionRelayEdge struct {
 	Node *FHIRComposition `json:"node,omitempty"`
 }
 
+// PagedFHIRComposition ...
+type PagedFHIRComposition struct {
+	Compositions    []FHIRComposition
+	HasNextPage     bool
+	NextCursor      string
+	HasPreviousPage bool
+	PreviousCursor  string
+	TotalCount      int
+}
+
 // FHIRCompositionRelayPayload is used to return single instances of Composition
 type FHIRCompositionRelayPayload struct {
 	Resource *FHIRComposition `json:"resource,omitempty"`

diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir.go
@@ -66,17 +66,11 @@ func NewFHIRStoreImpl(
 // SearchPatientObservations fetches all observations that belong to a specific patient
 func (fh StoreImpl) SearchPatientObservations(
 	_ context.Context,
-	patientReference string,
-	observationCode string,
+	searchParameters map[string]interface{},
 	tenant dto.TenantIdentifiers,
 	pagination dto.Pagination,
 ) (*domain.PagedFHIRObservations, error) {
-	params := map[string]interface{}{
-		"patient": patientReference,
-		"code":    observationCode,
-	}
-
-	observations, err := fh.Dataset.SearchFHIRResource(observationResourceType, params, tenant, pagination)
+	observations, err := fh.Dataset.SearchFHIRResource(observationResourceType, searchParameters, tenant, pagination)
 	if err != nil {
 		return nil, err
 	}
@@ -813,14 +807,21 @@ func (fh StoreImpl) UpdateFHIRAllergyIntolerance(_ context.Context, input domain
 }
 
 // SearchFHIRComposition provides a search API for FHIRComposition
-func (fh StoreImpl) SearchFHIRComposition(_ context.Context, params map[string]interface{}, tenant dto.TenantIdentifiers, pagination dto.Pagination) (*domain.FHIRCompositionRelayConnection, error) {
-	output := domain.FHIRCompositionRelayConnection{}
-
+func (fh StoreImpl) SearchFHIRComposition(_ context.Context, params map[string]interface{}, tenant dto.TenantIdentifiers, pagination dto.Pagination) (*domain.PagedFHIRComposition, error) {
 	resources, err := fh.Dataset.SearchFHIRResource(compositionResourceType, params, tenant, pagination)
 	if err != nil {
 		return nil, err
 	}
 
+	output := domain.PagedFHIRComposition{
+		Compositions:    []domain.FHIRComposition{},
+		HasNextPage:     resources.HasNextPage,
+		NextCursor:      resources.NextCursor,
+		HasPreviousPage: resources.HasPreviousPage,
+		PreviousCursor:  resources.PreviousCursor,
+		TotalCount:      resources.TotalCount,
+	}
+
 	for _, result := range resources.Resources {
 		var resource domain.FHIRComposition
 
@@ -835,9 +836,7 @@ func (fh StoreImpl) SearchFHIRComposition(_ context.Context, params map[string]i
 				"server error: Unable to unmarshal %s: %w", compositionResourceType, err)
 		}
 
-		output.Edges = append(output.Edges, &domain.FHIRCompositionRelayEdge{
-			Node: &resource,
-		})
+		output.Compositions = append(output.Compositions, resource)
 	}
 
 	return &output, nil

diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir_unit_test.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhir_unit_test.go
@@ -4053,11 +4053,10 @@ func TestStoreImpl_EndEpisode(t *testing.T) {
 func TestStoreImpl_SearchPatientObservations(t *testing.T) {
 	ctx := context.Background()
 	type args struct {
-		ctx              context.Context
-		patientReference string
-		observationCode  string
-		tenant           dto.TenantIdentifiers
-		pagination       dto.Pagination
+		ctx        context.Context
+		params     map[string]interface{}
+		tenant     dto.TenantIdentifiers
+		pagination dto.Pagination
 	}
 	tests := []struct {
 		name    string
@@ -4067,18 +4066,24 @@ func TestStoreImpl_SearchPatientObservations(t *testing.T) {
 		{
 			name: "Happy Case - Successfully search patient observation",
 			args: args{
-				ctx:              ctx,
-				patientReference: fmt.Sprintf("Patient/%s", gofakeit.UUID()),
-				observationCode:  "5088",
+				ctx: ctx,
+				params: map[string]interface{}{
+					"patient":         fmt.Sprintf("Patient/%s", gofakeit.UUID()),
+					"encounter":       fmt.Sprintf("Encounter/%s", gofakeit.UUID()),
+					"observationCode": "5088",
+				},
 			},
 			wantErr: false,
 		},
 		{
 			name: "Sad Case - fail to search fhir resource",
 			args: args{
-				ctx:              ctx,
-				patientReference: fmt.Sprintf("Patient/%s", gofakeit.UUID()),
-				observationCode:  "5088",
+				ctx: ctx,
+				params: map[string]interface{}{
+					"patient":         fmt.Sprintf("Patient/%s", gofakeit.UUID()),
+					"encounter":       fmt.Sprintf("Encounter/%s", gofakeit.UUID()),
+					"observationCode": "5088",
+				},
 			},
 			wantErr: true,
 		},
@@ -4093,8 +4098,7 @@ func TestStoreImpl_SearchPatientObservations(t *testing.T) {
 					return nil, fmt.Errorf("failed to search observation resource")
 				}
 			}
-
-			got, err := fh.SearchPatientObservations(tt.args.ctx, tt.args.patientReference, tt.args.observationCode, tt.args.tenant, tt.args.pagination)
+			got, err := fh.SearchPatientObservations(tt.args.ctx, tt.args.params, tt.args.tenant, tt.args.pagination)
 			if (err != nil) != tt.wantErr {
 				t.Errorf("StoreImpl.SearchPatientObservations() error = %v, wantErr %v", err, tt.wantErr)
 				return