refactor: move fhirdataset into cloudhealthcare

-  Created a folder called `cloudhealthcare` in the infrastructure layer. The folder will hold all implementations that are
specific to google cloud healthcare API.

.github/workflows/ci.yml

@@ -50,7 +50,7 @@ jobs:
 
       - name: Install Go dependencies
         run: |
-          curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(go env GOPATH)/bin v1.37.1
+          curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(go env GOPATH)/bin v1.50.1
           go get -u github.com/kisielk/errcheck
           go get -u golang.org/x/lint/golint
           go install honnef.co/go/tools/cmd/staticcheck@2021.1.2

pkg/clinical/application/common/testutils/testhelpers.go

@@ -5,8 +5,8 @@ import (
 
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
-	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhir"
-	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
+	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare"
+	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/openconceptlab"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases"
 	"github.com/savannahghi/firebasetools"
@@ -21,7 +21,7 @@ func InitializeTestService(ctx context.Context) (usecases.Interactor, error) {
 	fhir := fhir.NewFHIRStoreImpl(repo)
 	ocl := openconceptlab.NewServiceOCL()
 
-	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, repo, fhir, ocl)
+	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, fhir, ocl)
 
 	usecases := usecases.NewUsecasesInteractor(infrastructure)
 

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

@@ -14,8 +14,8 @@ import (
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
 	"github.com/savannahghi/clinical/pkg/clinical/domain"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
-	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhir"
-	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
+	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare"
+	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/openconceptlab"
 	"github.com/savannahghi/clinical/pkg/clinical/presentation/interactor"
 	"github.com/savannahghi/converterandformatter"
@@ -82,7 +82,7 @@ func InitializeTestInfrastructure(ctx context.Context) (infrastructure.Infrastru
 	fhir := fhir.NewFHIRStoreImpl(repo)
 
 	ocl := openconceptlab.NewServiceOCL()
-	return infrastructure.NewInfrastructureInteractor(baseExtension, repo, fhir, ocl), nil
+	return infrastructure.NewInfrastructureInteractor(baseExtension, fhir, ocl), nil
 }
 
 // func simplePatientRegistration() (*domain.SimplePatientRegistrationInput, error) {

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

@@ -4,6 +4,8 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
+	"io"
+	"net/http"
 	"net/url"
 	"time"
 
@@ -12,7 +14,7 @@ import (
 	"github.com/savannahghi/clinical/pkg/clinical/application/common/helpers"
 	"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"
+	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset"
 	"github.com/savannahghi/clinical/pkg/clinical/repository"
 	"github.com/savannahghi/converterandformatter"
 	"github.com/savannahghi/scalarutils"
@@ -1794,3 +1796,34 @@ func (fh *StoreImpl) SearchFHIRMedicationStatement(ctx context.Context, params m
 	}
 	return &output, nil
 }
+
+// CreateFHIRResource creates a FHIR resource
+func (fh *StoreImpl) CreateFHIRResource(resourceType string, payload map[string]interface{}) ([]byte, error) {
+	return fh.Dataset.CreateFHIRResource(resourceType, payload)
+}
+
+// PatchFHIRResource patches a FHIR resource
+func (fh *StoreImpl) PatchFHIRResource(resourceType, fhirResourceID string, payload []map[string]interface{}) ([]byte, error) {
+	return fh.Dataset.PatchFHIRResource(resourceType, fhirResourceID, payload)
+}
+
+// UpdateFHIRResource updates a FHIR resource
+func (fh *StoreImpl) UpdateFHIRResource(resourceType, fhirResourceID string, payload map[string]interface{}) ([]byte, error) {
+	return fh.Dataset.UpdateFHIRResource(resourceType, fhirResourceID, payload)
+}
+
+// POSTRequest is used to manually compose POST requests to the FHIR service
+func (fh *StoreImpl) POSTRequest(resourceName string, path string, params url.Values, body io.Reader) ([]byte, error) {
+	return fh.Dataset.POSTRequest(resourceName, path, params, body)
+}
+
+// GetFHIRResource gets a FHIR resource.
+func (fh *StoreImpl) GetFHIRResource(resourceType, fhirResourceID string) ([]byte, error) {
+	return fh.Dataset.GetFHIRResource(resourceType, fhirResourceID)
+}
+
+// FHIRHeaders composes suitable FHIR headers, with authentication and content
+// type already set
+func (fh *StoreImpl) FHIRHeaders() (http.Header, error) {
+	return fh.Dataset.FHIRHeaders()
+}

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

@@ -10,11 +10,11 @@ import (
 	"github.com/brianvoe/gofakeit"
 	"github.com/google/uuid"
 	"github.com/savannahghi/clinical/pkg/clinical/domain"
-	FHIR "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhir"
+	FHIR "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare"
 	"github.com/savannahghi/scalarutils"
 	"github.com/segmentio/ksuid"
 
-	fakeDataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset/mock"
+	fakeDataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset/mock"
 )
 
 func TestStoreImpl_CreateEpisodeOfCare_Unittest(t *testing.T) {

pkg/clinical/infrastructure/datastore/fhirdataset/dataset_test.go → pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset/dataset_test.go

@@ -6,7 +6,7 @@ import (
 	"strings"
 	"testing"
 
-	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
+	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset"
 	"github.com/tj/assert"
 )
 

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

@@ -2,6 +2,7 @@ package mock
 
 import (
 	"context"
+	"encoding/json"
 	"fmt"
 	"io"
 	"net/http"
@@ -67,6 +68,11 @@ type FHIRMock struct {
 	MockSearchFHIRMedicationStatementFn func(ctx context.Context, params map[string]interface{}) (*domain.FHIRMedicationStatementRelayConnection, error)
 	MockFHIRHeadersFn                   func() (http.Header, error)
 	MockGetBearerTokenFn                func() (string, error)
+
+	MockCreateFHIRResourceFn func(resourceType string, payload map[string]interface{}) ([]byte, error)
+	MockPatchFHIRResourceFn  func(resourceType, fhirResourceID string, payload []map[string]interface{}) ([]byte, error)
+	MockUpdateFHIRResourceFn func(resourceType, fhirResourceID string, payload map[string]interface{}) ([]byte, error)
+	MockGetFHIRResourceFn    func(resourceType, fhirResourceID string) ([]byte, error)
 }
 
 // NewFHIRMock initializes a new instance of FHIR mock
@@ -145,7 +151,17 @@ func NewFHIRMock() *FHIRMock {
 			return &domain.FHIROrganizationRelayConnection{}, nil
 		},
 		MockPOSTRequestFn: func(resourceName string, path string, params url.Values, body io.Reader) ([]byte, error) {
-			return []byte("m"), nil
+			m := map[string]string{
+				"resourceType": "Bundle",
+				"type":         "searchset",
+				"total":        "10",
+				"link":         "test",
+			}
+			bs, err := json.Marshal(m)
+			if err != nil {
+				return nil, fmt.Errorf("unable to marshal map to JSON: %w", err)
+			}
+			return bs, nil
 		},
 		MockSearchEpisodesByParamFn: func(ctx context.Context, searchParams url.Values) ([]*domain.FHIREpisodeOfCare, error) {
 			return []*domain.FHIREpisodeOfCare{}, nil
@@ -386,6 +402,55 @@ func NewFHIRMock() *FHIRMock {
 		MockGetBearerTokenFn: func() (string, error) {
 			return fmt.Sprintf("Bearer %s", uuid.NewString()), nil
 		},
+		MockCreateFHIRResourceFn: func(resourceType string, payload map[string]interface{}) ([]byte, error) {
+			m := map[string]interface{}{
+				"key": "value",
+			}
+			bs, err := json.Marshal(m)
+			if err != nil {
+				return nil, fmt.Errorf("unable to marshal map to JSON: %w", err)
+			}
+			return bs, nil
+		},
+		MockPatchFHIRResourceFn: func(resourceType, fhirResourceID string, payload []map[string]interface{}) ([]byte, error) {
+			m := map[string]interface{}{
+				"key": "value",
+			}
+			bs, err := json.Marshal(m)
+			if err != nil {
+				return nil, fmt.Errorf("unable to marshal map to JSON: %w", err)
+			}
+			return bs, nil
+		},
+		MockUpdateFHIRResourceFn: func(resourceType, fhirResourceID string, payload map[string]interface{}) ([]byte, error) {
+			m := map[string]interface{}{
+				"key": "value",
+			}
+			bs, err := json.Marshal(m)
+			if err != nil {
+				return nil, fmt.Errorf("unable to marshal map to JSON: %w", err)
+			}
+			return bs, nil
+		},
+		MockGetFHIRResourceFn: func(resourceType, fhirResourceID string) ([]byte, error) {
+			n := map[string]interface{}{"given": []string{"John"}, "family": []string{"Doe"}}
+			p := map[string]interface{}{
+				"resourceType": "Patient/",
+				"id":           "test-UUID",
+				"name":         []map[string]interface{}{n},
+			}
+			m := map[string]interface{}{
+				"resourceType":  "Patient/",
+				"status":        "active",
+				"id":            "test-UUID",
+				"patientRecord": p,
+			}
+			bs, err := json.Marshal(m)
+			if err != nil {
+				return nil, fmt.Errorf("unable to marshal map to JSON: %w", err)
+			}
+			return bs, nil
+		},
 	}
 }
 
@@ -629,3 +694,23 @@ func (fh *FHIRMock) CreateFHIRMedication(ctx context.Context, input domain.FHIRM
 func (fh *FHIRMock) FHIRHeaders() (http.Header, error) {
 	return fh.MockFHIRHeadersFn()
 }
+
+// CreateFHIRResource mocks the implementation for creating a fhir resource
+func (fh *FHIRMock) CreateFHIRResource(resourceType string, payload map[string]interface{}) ([]byte, error) {
+	return fh.MockCreateFHIRResourceFn(resourceType, payload)
+}
+
+// PatchFHIRResource mocks the implementation for patching a fhir resource
+func (fh *FHIRMock) PatchFHIRResource(resourceType, fhirResourceID string, payload []map[string]interface{}) ([]byte, error) {
+	return fh.MockPatchFHIRResourceFn(resourceType, fhirResourceID, payload)
+}
+
+// UpdateFHIRResource mocks the implementation for updating a FHIR resource
+func (fh *FHIRMock) UpdateFHIRResource(resourceType, fhirResourceID string, payload map[string]interface{}) ([]byte, error) {
+	return fh.MockUpdateFHIRResourceFn(resourceType, fhirResourceID, payload)
+}
+
+// GetFHIRResource mocks the implementation of getting a FHIR resource
+func (fh *FHIRMock) GetFHIRResource(resourceType, fhirResourceID string) ([]byte, error) {
+	return fh.MockGetFHIRResourceFn(resourceType, fhirResourceID)
+}

pkg/clinical/infrastructure/infrastructure.go

@@ -3,15 +3,13 @@ package infrastructure
 import (
 	"github.com/savannahghi/clinical/pkg/clinical/application/common"
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
-	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           repository.FHIR
 	OpenConceptLab openconceptlab.ServiceOCL
 	BaseExtension  extensions.BaseExtension
@@ -21,15 +19,13 @@ type Infrastructure struct {
 // NewInfrastructureInteractor initializes a new Infrastructure
 func NewInfrastructureInteractor(
 	ext extensions.BaseExtension,
-	fhirRepository dataset.FHIRRepository,
 	fhir repository.FHIR,
 	openconceptlab openconceptlab.ServiceOCL,
 ) Infrastructure {
 	myCareHubClient := common.NewInterServiceClient("mycarehub", ext)
 	mycarehub := mycarehub.NewServiceMyCareHub(myCareHubClient, ext)
 
 	return Infrastructure{
-		fhirRepository,
 		fhir,
 		openconceptlab,
 		ext,

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

@@ -9,8 +9,8 @@ import (
 	"cloud.google.com/go/pubsub"
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
-	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhir"
-	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
+	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare"
+	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/openconceptlab"
 	pubsubmessaging "github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/pubsub"
 	"github.com/savannahghi/clinical/pkg/clinical/usecases"
@@ -41,7 +41,7 @@ func InitializeTestPubSub(t *testing.T) (*pubsubmessaging.ServicePubSubMessaging
 	fhir := fhir.NewFHIRStoreImpl(repo)
 	ocl := openconceptlab.NewServiceOCL()
 
-	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, repo, fhir, ocl)
+	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, fhir, ocl)
 	usecases := usecases.NewUsecasesInteractor(infrastructure)
 	oclUseCase := usecases.UseCasesOCL
 	pubSub, err := pubsubmessaging.NewServicePubSubMessaging(

pkg/clinical/presentation/config.go

@@ -16,8 +16,8 @@ import (
 	"github.com/savannahghi/authutils"
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
-	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhir"
-	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/fhirdataset"
+	fhir "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare"
+	dataset "github.com/savannahghi/clinical/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/openconceptlab"
 	pubsubmessaging "github.com/savannahghi/clinical/pkg/clinical/infrastructure/services/pubsub"
 	"github.com/savannahghi/clinical/pkg/clinical/presentation/graph"
@@ -120,7 +120,7 @@ func Router(ctx context.Context) (*mux.Router, error) {
 	fhir := fhir.NewFHIRStoreImpl(repo)
 	ocl := openconceptlab.NewServiceOCL()
 
-	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, repo, fhir, ocl)
+	infrastructure := infrastructure.NewInfrastructureInteractor(baseExtension, fhir, ocl)
 	usecases := usecases.NewUsecasesInteractor(infrastructure)
 	h := rest.NewPresentationHandlers(usecases)
 

pkg/clinical/repository/repository.go

@@ -2,6 +2,8 @@ package repository
 
 import (
 	"context"
+	"io"
+	"net/http"
 	"net/url"
 
 	"github.com/savannahghi/clinical/pkg/clinical/domain"
@@ -60,4 +62,11 @@ type FHIR interface {
 	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)
+
+	CreateFHIRResource(resourceType string, payload map[string]interface{}) ([]byte, error)
+	PatchFHIRResource(resourceType, fhirResourceID string, payload []map[string]interface{}) ([]byte, error)
+	UpdateFHIRResource(resourceType, fhirResourceID string, payload map[string]interface{}) ([]byte, error)
+	POSTRequest(resourceName string, path string, params url.Values, body io.Reader) ([]byte, error)
+	GetFHIRResource(resourceType, fhirResourceID string) ([]byte, error)
+	FHIRHeaders() (http.Header, error)
 }

pkg/clinical/usecases/clinical/fhir.go

@@ -221,7 +221,7 @@ func (c *UseCasesClinicalImpl) SearchEpisodesByParam(ctx context.Context, search
 // - `path` is a sub-path e.g `_search` under a resource
 // - `params` should be query params, sent as `url.Values`
 func (c *UseCasesClinicalImpl) POSTRequest(resourceName string, path string, params url.Values, body io.Reader) ([]byte, error) {
-	return c.infrastructure.FHIRRepo.POSTRequest(resourceName, path, params, body)
+	return c.infrastructure.FHIR.POSTRequest(resourceName, path, params, body)
 }
 
 // OpenEpisodes returns the IDs of a patient's open episodes
@@ -241,7 +241,7 @@ func (c *UseCasesClinicalImpl) HasOpenEpisode(
 // FHIRHeaders composes suitable FHIR headers, with authentication and content
 // type already set
 func (c *UseCasesClinicalImpl) FHIRHeaders() (http.Header, error) {
-	return c.infrastructure.FHIRRepo.FHIRHeaders()
+	return c.infrastructure.FHIR.FHIRHeaders()
 }
 
 // CreateFHIREncounter creates a FHIREncounter instance
@@ -334,7 +334,7 @@ func (c *UseCasesClinicalImpl) UpgradeEpisode(ctx context.Context, input domain.
 		return nil, fmt.Errorf("unable to turn episode of care input into a map: %v", err)
 	}
 
-	_, err = c.infrastructure.FHIRRepo.UpdateFHIRResource(
+	_, err = c.infrastructure.FHIR.UpdateFHIRResource(
 		"EpisodeOfCare", *episode.ID, payload)
 	if err != nil {
 		utils.ReportErrorToSentry(err)