refactor: combine clinical and fhir usecase

Dockerfile

@@ -30,8 +30,5 @@ RUN apk add --no-cache ca-certificates
 COPY --from=builder /app/server /server
 COPY --from=builder /app/deps.yaml /deps.yaml
 
-COPY --from=builder /app/pkg/clinical/application/authorization/rbac_model.conf /app/pkg/clinical/application/authorization/rbac_model.conf
-COPY --from=builder /app/pkg/clinical/application/authorization/data/rbac_policy.csv /app/pkg/clinical/application/authorization/data/rbac_policy.csv
-
 # Run the web service on container startup.
 CMD ["/server"]

go.mod

@@ -9,7 +9,6 @@ require (
 	github.com/ahmetb/go-linq/v3 v3.2.0
 	github.com/asaskevich/govalidator v0.0.0-20210307081110-f21760c49a8d
 	github.com/brianvoe/gofakeit v3.18.0+incompatible
-	github.com/casbin/casbin/v2 v2.44.3
 	github.com/getsentry/sentry-go v0.13.0
 	github.com/google/uuid v1.3.0
 	github.com/gorilla/handlers v1.5.1

go.sum

@@ -93,8 +93,6 @@ github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym
 github.com/CloudyKit/fastprinter v0.0.0-20200109182630-33d98a066a53/go.mod h1:+3IMCy2vIlbG1XG/0ggNQv0SvxCAIpPM5b1nCz56Xno=
 github.com/CloudyKit/jet/v3 v3.0.0/go.mod h1:HKQPgSJmdK8hdoAbKUUWajkHyHo4RaU5rMdUywE7VMo=
 github.com/Joker/hpp v1.0.0/go.mod h1:8x5n+M1Hp5hC0g8okX3sR3vFQwynaX/UgSOM9MeBKzY=
-github.com/Knetic/govaluate v3.0.1-0.20171022003610-9aa49832a739+incompatible h1:1G1pk05UrOh0NlF1oeaaix1x8XzrfjIDK47TY0Zehcw=
-github.com/Knetic/govaluate v3.0.1-0.20171022003610-9aa49832a739+incompatible/go.mod h1:r7JcOSlj0wfOMncg0iLm8Leh48TZaKVeNIfJntJ2wa0=
 github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU=
 github.com/Shopify/goreferrer v0.0.0-20181106222321-ec9c9a553398/go.mod h1:a1uqRtAwp2Xwc6WNPJEufxJ7fx3npB4UV/JOLmbu5I0=
 github.com/agnivade/levenshtein v1.0.1/go.mod h1:CURSv5d9Uaml+FovSIICkLbAUZ9S4RqaHDIsdSBg7lM=
@@ -117,8 +115,6 @@ github.com/aws/aws-sdk-go v1.37.0/go.mod h1:hcU610XS61/+aQV88ixoOzUoG7v3b31pl2zK
 github.com/aymerick/raymond v2.0.3-0.20180322193309-b565731e1464+incompatible/go.mod h1:osfaiScAUVup+UC9Nfq76eWqDhXlp+4UYaA8uhTBO6g=
 github.com/brianvoe/gofakeit v3.18.0+incompatible h1:wDOmHc9DLG4nRjUVVaxA+CEglKOW72Y5+4WNxUIkjM8=
 github.com/brianvoe/gofakeit v3.18.0+incompatible/go.mod h1:kfwdRA90vvNhPutZWfH7WPaDzUjz+CZFqG+rPkOjGOc=
-github.com/casbin/casbin/v2 v2.44.3 h1:tPP1YypfG2fqe7S2zivYuD11yc+/mc0GXJe/sDVbb1U=
-github.com/casbin/casbin/v2 v2.44.3/go.mod h1:vByNa/Fchek0KZUgG5wEsl7iFsiviAYKRtgrQfcJqHg=
 github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=
 github.com/census-instrumentation/opencensus-proto v0.3.0 h1:t/LhUZLVitR1Ow2YOnduCsavhwFUklBMoGVYUCqmCqk=
 github.com/census-instrumentation/opencensus-proto v0.3.0/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=

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

@@ -13,6 +13,7 @@ import (
 	"github.com/savannahghi/clinical/pkg/clinical/application/utils"
 	"github.com/savannahghi/clinical/pkg/clinical/domain"
 	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
+	"github.com/savannahghi/clinical/pkg/clinical/repository"
 	"github.com/savannahghi/converterandformatter"
 	"github.com/savannahghi/scalarutils"
 )
@@ -23,61 +24,6 @@ const (
 	timeFormatStr = "2006-01-02T15:04:05+03:00"
 )
 
-// FHIR represents all the FHIR logic
-type FHIR interface {
-	CreateEpisodeOfCare(ctx context.Context, episode domain.FHIREpisodeOfCare) (*domain.EpisodeOfCarePayload, error)
-	SearchFHIRCondition(ctx context.Context, params map[string]interface{}) (*domain.FHIRConditionRelayConnection, error)
-	CreateFHIRCondition(ctx context.Context, input domain.FHIRConditionInput) (*domain.FHIRConditionRelayPayload, error)
-	CreateFHIROrganization(ctx context.Context, input domain.FHIROrganizationInput) (*domain.FHIROrganizationRelayPayload, error)
-	SearchFHIROrganization(ctx context.Context, params map[string]interface{}) (*domain.FHIROrganizationRelayConnection, error)
-	FindOrganizationByID(ctx context.Context, organisationID string) (*domain.FHIROrganizationRelayPayload, error)
-	SearchEpisodesByParam(ctx context.Context, searchParams url.Values) ([]*domain.FHIREpisodeOfCare, error)
-	HasOpenEpisode(
-		ctx context.Context,
-		patient domain.FHIRPatient,
-	) (bool, error)
-	OpenEpisodes(
-		ctx context.Context, patientReference string) ([]*domain.FHIREpisodeOfCare, error)
-	CreateFHIREncounter(ctx context.Context, input domain.FHIREncounterInput) (*domain.FHIREncounterRelayPayload, error)
-	GetFHIREpisodeOfCare(ctx context.Context, id string) (*domain.FHIREpisodeOfCareRelayPayload, error)
-	Encounters(ctx context.Context, patientReference string, status *domain.EncounterStatusEnum) ([]*domain.FHIREncounter, error)
-	SearchFHIREpisodeOfCare(ctx context.Context, params map[string]interface{}) (*domain.FHIREpisodeOfCareRelayConnection, error)
-	StartEncounter(ctx context.Context, episodeID string) (string, error)
-	SearchEpisodeEncounter(
-		ctx context.Context,
-		episodeReference string,
-	) (*domain.FHIREncounterRelayConnection, error)
-	EndEncounter(ctx context.Context, encounterID string) (bool, error)
-	EndEpisode(ctx context.Context, episodeID string) (bool, error)
-	GetActiveEpisode(ctx context.Context, episodeID string) (*domain.FHIREpisodeOfCare, error)
-	SearchFHIRServiceRequest(ctx context.Context, params map[string]interface{}) (*domain.FHIRServiceRequestRelayConnection, error)
-	CreateFHIRServiceRequest(ctx context.Context, input domain.FHIRServiceRequestInput) (*domain.FHIRServiceRequestRelayPayload, error)
-	SearchFHIRAllergyIntolerance(ctx context.Context, params map[string]interface{}) (*domain.FHIRAllergyIntoleranceRelayConnection, error)
-	CreateFHIRAllergyIntolerance(ctx context.Context, input domain.FHIRAllergyIntoleranceInput) (*domain.FHIRAllergyIntoleranceRelayPayload, error)
-	UpdateFHIRAllergyIntolerance(ctx context.Context, input domain.FHIRAllergyIntoleranceInput) (*domain.FHIRAllergyIntoleranceRelayPayload, error)
-	SearchFHIRComposition(ctx context.Context, params map[string]interface{}) (*domain.FHIRCompositionRelayConnection, error)
-	CreateFHIRComposition(ctx context.Context, input domain.FHIRCompositionInput) (*domain.FHIRCompositionRelayPayload, error)
-	UpdateFHIRComposition(ctx context.Context, input domain.FHIRCompositionInput) (*domain.FHIRCompositionRelayPayload, error)
-	DeleteFHIRComposition(ctx context.Context, id string) (bool, error)
-	UpdateFHIRCondition(ctx context.Context, input domain.FHIRConditionInput) (*domain.FHIRConditionRelayPayload, error)
-	GetFHIREncounter(ctx context.Context, id string) (*domain.FHIREncounterRelayPayload, error)
-	SearchFHIREncounter(ctx context.Context, params map[string]interface{}) (*domain.FHIREncounterRelayConnection, error)
-	SearchFHIRMedicationRequest(ctx context.Context, params map[string]interface{}) (*domain.FHIRMedicationRequestRelayConnection, error)
-	CreateFHIRMedicationRequest(ctx context.Context, input domain.FHIRMedicationRequestInput) (*domain.FHIRMedicationRequestRelayPayload, error)
-	UpdateFHIRMedicationRequest(ctx context.Context, input domain.FHIRMedicationRequestInput) (*domain.FHIRMedicationRequestRelayPayload, error)
-	DeleteFHIRMedicationRequest(ctx context.Context, id string) (bool, error)
-	SearchFHIRObservation(ctx context.Context, params map[string]interface{}) (*domain.FHIRObservationRelayConnection, error)
-	CreateFHIRObservation(ctx context.Context, input domain.FHIRObservationInput) (*domain.FHIRObservationRelayPayload, error)
-	DeleteFHIRObservation(ctx context.Context, id string) (bool, error)
-	GetFHIRPatient(ctx context.Context, id string) (*domain.FHIRPatientRelayPayload, error)
-	DeleteFHIRPatient(ctx context.Context, id string) (bool, error)
-	DeleteFHIRServiceRequest(ctx context.Context, id string) (bool, error)
-	DeleteFHIRResourceType(results []map[string]string) error
-	CreateFHIRMedicationStatement(ctx context.Context, input domain.FHIRMedicationStatementInput) (*domain.FHIRMedicationStatementRelayPayload, error)
-	CreateFHIRMedication(ctx context.Context, input domain.FHIRMedicationInput) (*domain.FHIRMedicationRelayPayload, error)
-	SearchFHIRMedicationStatement(ctx context.Context, params map[string]interface{}) (*domain.FHIRMedicationStatementRelayConnection, error)
-}
-
 // StoreImpl represents the FHIR infrastructure implementation
 type StoreImpl struct {
 	Dataset dataset.FHIRRepository
@@ -86,7 +32,7 @@ type StoreImpl struct {
 // NewFHIRStoreImpl initializes the new FHIR implementation
 func NewFHIRStoreImpl(
 	dataset dataset.FHIRRepository,
-) FHIR {
+) repository.FHIR {
 	return &StoreImpl{
 		Dataset: dataset,
 	}

pkg/clinical/infrastructure/infrastructure.go

@@ -3,16 +3,16 @@ package infrastructure
 import (
 	"github.com/savannahghi/clinical/pkg/clinical/application/common"
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
-	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhir"
 	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/mycarehub"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/openconceptlab"
+	"github.com/savannahghi/clinical/pkg/clinical/repository"
 )
 
 // Infrastructure ...
 type Infrastructure struct {
 	FHIRRepo       dataset.FHIRRepository
-	FHIR           fhir.FHIR
+	FHIR           repository.FHIR
 	OpenConceptLab openconceptlab.ServiceOCL
 	BaseExtension  extensions.BaseExtension
 	MyCareHub      mycarehub.IServiceMyCareHub
@@ -22,7 +22,7 @@ type Infrastructure struct {
 func NewInfrastructureInteractor(
 	ext extensions.BaseExtension,
 	fhirRepository dataset.FHIRRepository,
-	fhir fhir.FHIR,
+	fhir repository.FHIR,
 	openconceptlab openconceptlab.ServiceOCL,
 ) Infrastructure {
 	myCareHubClient := common.NewInterServiceClient("mycarehub", ext)

pkg/clinical/infrastructure/services/pubsub/service.go

@@ -10,7 +10,6 @@ import (
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases/clinical"
-	fhirUsecase "github.com/savannahghi/clinical/pkg/clinical/usecases/fhir"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases/ocl"
 	"github.com/savannahghi/serverutils"
 )
@@ -57,30 +56,27 @@ type ServicePubsub interface {
 
 // ServicePubSubMessaging is used to send and receive pubsub notifications
 type ServicePubSubMessaging struct {
-	client  *pubsub.Client
-	baseExt extensions.BaseExtension
-	infra   infrastructure.Infrastructure
-	patient clinical.UseCasesClinical
-	fhir    fhirUsecase.UseCasesFHIR
-	ocl     ocl.UseCasesOCL
+	client   *pubsub.Client
+	baseExt  extensions.BaseExtension
+	infra    infrastructure.Infrastructure
+	clinical clinical.UseCasesClinical
+	ocl      ocl.UseCasesOCL
 }
 
 // NewServicePubSubMessaging returns a new instance of pubsub
 func NewServicePubSubMessaging(
 	client *pubsub.Client,
 	baseExt extensions.BaseExtension,
 	infra infrastructure.Infrastructure,
-	patient clinical.UseCasesClinical,
-	fhir fhirUsecase.UseCasesFHIR,
+	clinical clinical.UseCasesClinical,
 	ocl ocl.UseCasesOCL,
 ) (*ServicePubSubMessaging, error) {
 	s := &ServicePubSubMessaging{
-		client:  client,
-		baseExt: baseExt,
-		infra:   infra,
-		patient: patient,
-		fhir:    fhir,
-		ocl:     ocl,
+		client:   client,
+		baseExt:  baseExt,
+		infra:    infra,
+		clinical: clinical,
+		ocl:      ocl,
 	}
 
 	ctx := context.Background()

pkg/clinical/infrastructure/services/pubsub/service_test.go

@@ -49,7 +49,6 @@ func InitializeTestPubSub(t *testing.T) (*pubsubmessaging.ServicePubSubMessaging
 		baseExtension,
 		infrastructure,
 		usecases,
-		usecases,
 		oclUseCase,
 	)
 	if err != nil {

pkg/clinical/infrastructure/services/pubsub/subscriber.go

@@ -84,7 +84,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			Active:       profile.Active,
 		}
 
-		patient, err := ps.patient.RegisterPatient(ctx, payload)
+		patient, err := ps.clinical.RegisterPatient(ctx, payload)
 		if err != nil {
 			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
 				Err:     err,
@@ -131,7 +131,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			},
 		}
 
-		response, err := ps.fhir.CreateFHIROrganization(ctx, input)
+		response, err := ps.clinical.CreateFHIROrganization(ctx, input)
 		if err != nil {
 			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
 				Err:     err,
@@ -168,7 +168,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			return
 		}
 
-		_, err = ps.fhir.CreateFHIRObservation(ctx, *input)
+		_, err = ps.clinical.CreateFHIRObservation(ctx, *input)
 		if err != nil {
 			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
 				Err:     err,
@@ -197,7 +197,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			return
 		}
 
-		_, err = ps.fhir.CreateFHIRAllergyIntolerance(ctx, *input)
+		_, err = ps.clinical.CreateFHIRAllergyIntolerance(ctx, *input)
 		if err != nil {
 			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
 				Err:     err,
@@ -226,7 +226,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			return
 		}
 
-		_, err = ps.fhir.CreateFHIRMedicationStatement(ctx, *input)
+		_, err = ps.clinical.CreateFHIRMedicationStatement(ctx, *input)
 		if err != nil {
 			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
 				Err:     err,
@@ -255,7 +255,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 			return
 		}
 
-		_, err = ps.fhir.CreateFHIRObservation(ctx, *input)
+		_, err = ps.clinical.CreateFHIRObservation(ctx, *input)
 		if err != nil {
 			serverutils.WriteJSONResponse(w, errorcodeutil.CustomError{
 				Err:     err,
@@ -280,7 +280,7 @@ func (ps ServicePubSubMessaging) ReceivePubSubPushMessages(
 // ComposeTestResultInput composes a test result input from data received
 func (ps ServicePubSubMessaging) ComposeTestResultInput(ctx context.Context, input dto.CreatePatientTestResultPubSubMessage) (*domain.FHIRObservationInput, error) {
 	var patientName string
-	patient, err := ps.patient.FindPatientByID(ctx, input.PatientID)
+	patient, err := ps.clinical.FindPatientByID(ctx, input.PatientID)
 	if err != nil {
 		return nil, err
 	}
@@ -329,7 +329,7 @@ func (ps ServicePubSubMessaging) ComposeTestResultInput(ctx context.Context, inp
 	}
 
 	if input.OrganizationID != "" {
-		organization, err := ps.fhir.FindOrganizationByID(ctx, input.OrganizationID) // rename organization response
+		organization, err := ps.clinical.FindOrganizationByID(ctx, input.OrganizationID) // rename organization response
 		if err != nil {
 			//Should not fail if the organization is not found
 			log.Printf("the error is: %v", err)
@@ -387,7 +387,7 @@ func (ps ServicePubSubMessaging) ComposeVitalsInput(ctx context.Context, input d
 		ValueString: &input.Value,
 	}
 
-	patient, err := ps.patient.FindPatientByID(ctx, input.PatientID)
+	patient, err := ps.clinical.FindPatientByID(ctx, input.PatientID)
 	if err != nil {
 		return nil, err
 	}
@@ -399,7 +399,7 @@ func (ps ServicePubSubMessaging) ComposeVitalsInput(ctx context.Context, input d
 	}
 
 	if input.OrganizationID != "" {
-		organization, err := ps.fhir.FindOrganizationByID(ctx, input.OrganizationID)
+		organization, err := ps.clinical.FindOrganizationByID(ctx, input.OrganizationID)
 		if err != nil {
 			//Should not fail if organization is not found
 			log.Printf("the error is: %v", err)
@@ -462,7 +462,7 @@ func (ps ServicePubSubMessaging) ComposeMedicationStatementInput(ctx context.Con
 		},
 	}
 
-	patient, err := ps.patient.FindPatientByID(ctx, input.PatientID)
+	patient, err := ps.clinical.FindPatientByID(ctx, input.PatientID)
 	if err != nil {
 		return nil, err
 	}
@@ -474,7 +474,7 @@ func (ps ServicePubSubMessaging) ComposeMedicationStatementInput(ctx context.Con
 	}
 
 	if input.OrganizationID != "" {
-		organization, err := ps.fhir.FindOrganizationByID(ctx, input.OrganizationID) // rename organization response
+		organization, err := ps.clinical.FindOrganizationByID(ctx, input.OrganizationID) // rename organization response
 		if err != nil {
 			log.Printf("the error is: %v", err)
 		}
@@ -530,7 +530,7 @@ func (ps ServicePubSubMessaging) ComposeAllergyIntoleranceInput(ctx context.Cont
 		Day:   day,
 	}
 
-	patient, err := ps.patient.FindPatientByID(ctx, input.PatientID)
+	patient, err := ps.clinical.FindPatientByID(ctx, input.PatientID)
 	if err != nil {
 		return nil, err
 	}

pkg/clinical/presentation/config.go

@@ -122,9 +122,9 @@ func Router(ctx context.Context) (*mux.Router, error) {
 
 	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, repo, fhir, ocl)
 	usecases := usecases.NewUsecasesInteractor(infrastructure)
-	h := rest.NewPresentationHandlers(infrastructure, usecases)
+	h := rest.NewPresentationHandlers(usecases)
 
-	pubSub, err := pubsubmessaging.NewServicePubSubMessaging(pubSubClient, baseExtension, infrastructure, usecases, usecases, ocl)
+	pubSub, err := pubsubmessaging.NewServicePubSubMessaging(pubSubClient, baseExtension, infrastructure, usecases, ocl)
 	if err != nil {
 		return nil, fmt.Errorf("failed to initialize pubsub messaging service: %v", err)
 	}

pkg/clinical/presentation/interactor/interactor.go

@@ -3,21 +3,18 @@ package interactor
 import (
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases/clinical"
-	fhir "github.com/savannahghi/clinical/pkg/clinical/usecases/fhir"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases/ocl"
 )
 
 // Usecases is an interface that combines of all usescases
 type Usecases interface {
 	clinical.UseCasesClinical
-	fhir.UseCasesFHIR
 	ocl.UseCasesOCL
 }
 
 // Interactor is an implementation of the usecases interface
 type Interactor struct {
 	clinical.UseCasesClinical
-	fhir.UseCasesFHIR
 	infrastructure.Infrastructure
 	ocl.UseCasesOCL
 }
@@ -27,12 +24,10 @@ func NewUsecasesInteractor(
 	infrastructure infrastructure.Infrastructure,
 ) Usecases {
 	clinical := clinical.NewUseCasesClinicalImpl(infrastructure)
-	fhir := fhir.NewUseCasesFHIRImpl(infrastructure)
 	ocl := ocl.NewUseCasesOCLImpl(infrastructure)
 
 	impl := &Interactor{
 		clinical,
-		fhir,
 		infrastructure,
 		ocl,
 	}

pkg/clinical/presentation/rest/handlers.go

@@ -6,7 +6,6 @@ import (
 
 	"github.com/savannahghi/clinical/pkg/clinical/application/utils"
 	"github.com/savannahghi/clinical/pkg/clinical/domain"
-	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases"
 	"github.com/savannahghi/serverutils"
 )
@@ -18,13 +17,12 @@ type PresentationHandlers interface {
 
 // PresentationHandlersImpl represents the usecase implementation object
 type PresentationHandlersImpl struct {
-	usecases       usecases.Interactor
-	infrastructure infrastructure.Infrastructure
+	usecases usecases.Interactor
 }
 
 // NewPresentationHandlers initializes a new rest handlers usecase
-func NewPresentationHandlers(infrastructure infrastructure.Infrastructure, usecases usecases.Interactor) PresentationHandlers {
-	return &PresentationHandlersImpl{infrastructure: infrastructure, usecases: usecases}
+func NewPresentationHandlers(usecases usecases.Interactor) PresentationHandlers {
+	return &PresentationHandlersImpl{usecases: usecases}
 }
 
 // DeleteFHIRPatientByPhone handler exposes an endpoint that takes a