chore: refactor dataset.go

savannahghi · Mar 8, 2023 · 175fc8f · 175fc8f
1 parent 74a97f8
commit 175fc8f
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Showing 9 changed files with 111 additions and 236 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -18,6 +18,7 @@ env:
   OPENCONCEPTLAB_API_URL: ${{ secrets.OPENCONCEPTLAB_API_URL }}
   JWT_KEY: ${{ secrets.JWT_KEY }}
   CLOUD_HEALTH_FHIRSTORE_ID: ${{ secrets.CLOUD_HEALTH_FHIRSTORE_ID }}
+  CLOUD_HEALTH_DATASET_LOCATION: ${{ secrets.CLOUD_HEALTH_DATASET_LOCATION }}
   SENTRY_DSN: ${{ secrets.SENTRY_DSN }}
   SAVANNAH_ADMIN_EMAIL: ${{ secrets.SAVANNAH_ADMIN_EMAIL }}
   AUTHSERVER_ENDPOINT: ${{ secrets.AUTHSERVER_ENDPOINT }}

diff --git a/.github/workflows/staging_multitenant.yaml b/.github/workflows/staging_multitenant.yaml
@@ -48,6 +48,7 @@ jobs:
             CLOUD_HEALTH_PUBSUB_TOPIC=${{ secrets.CLOUD_HEALTH_PUBSUB_TOPIC }}
             CLOUD_HEALTH_DATASET_ID=${{ secrets.CLOUD_HEALTH_DATASET_ID }}
             CLOUD_HEALTH_FHIRSTORE_ID=${{ secrets.CLOUD_HEALTH_FHIRSTORE_ID }}
+            CLOUD_HEALTH_DATASET_LOCATION=${{ secrets.CLOUD_HEALTH_DATASET_LOCATION }}
             OPENCONCEPTLAB_TOKEN=${{ secrets.OPENCONCEPTLAB_TOKEN }}
             SERVICE_HOST=${{ secrets.SERVICE_HOST }}
             OPENCONCEPTLAB_API_URL=${{ secrets.OPENCONCEPTLAB_API_URL }}

diff --git a/pkg/clinical/application/common/testutils/testhelpers.go b/pkg/clinical/application/common/testutils/testhelpers.go
@@ -2,20 +2,34 @@ package testutils
 
 import (
 	"context"
+	"log"
 
 	"github.com/savannahghi/clinical/pkg/clinical/application/extensions"
 	"github.com/savannahghi/clinical/pkg/clinical/infrastructure"
 	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/serverutils"
+	"google.golang.org/api/healthcare/v1"
 )
 
 // InitializeTestService sets up the structure that will be used by the usecase layer for
 // integration tests
 func InitializeTestService(ctx context.Context) (usecases.Interactor, error) {
+	project := serverutils.MustGetEnvVar(serverutils.GoogleCloudProjectIDEnvVarName)
+	_ = serverutils.MustGetEnvVar("CLOUD_HEALTH_PUBSUB_TOPIC")
+	datasetID := serverutils.MustGetEnvVar("CLOUD_HEALTH_DATASET_ID")
+	datasetLocation := serverutils.MustGetEnvVar("CLOUD_HEALTH_DATASET_LOCATION")
+	fhirStoreID := serverutils.MustGetEnvVar("CLOUD_HEALTH_FHIRSTORE_ID")
+	hsv, err := healthcare.NewService(ctx)
+	if err != nil {
+		log.Panicf("unable to initialize new Google Cloud Healthcare Service: %s", err)
+	}
+
+	repo := dataset.NewFHIRRepository(ctx, hsv, project, datasetID, datasetLocation, fhirStoreID)
+
 	baseExtension := extensions.NewBaseExtensionImpl()
-	repo := dataset.NewFHIRRepository(ctx)
 	fhir := fhir.NewFHIRStoreImpl(repo)
 	ocl := openconceptlab.NewServiceOCL()
 

diff --git a/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset/dataset.go b/pkg/clinical/infrastructure/datastore/cloudhealthcare/fhirdataset/dataset.go
@@ -19,7 +19,6 @@ import (
 
 // constants used to configure the Google Cloud Healthcare API
 const (
-	DatasetLocation       = "europe-west4"
 	baseFHIRURL           = "https://healthcare.googleapis.com/v1"
 	defaultTimeoutSeconds = 10
 )
@@ -29,33 +28,30 @@ const (
 type Repository struct {
 	healthcareService                           *healthcare.Service
 	projectID, location, datasetID, fhirStoreID string
+	parent                                      string
+	datasetName                                 string
+	fhirStoreName                               string
 }
 
 // NewFHIRRepository initializes a FHIR repository
-func NewFHIRRepository(ctx context.Context) *Repository {
-	project := serverutils.MustGetEnvVar(serverutils.GoogleCloudProjectIDEnvVarName)
-	_ = serverutils.MustGetEnvVar("CLOUD_HEALTH_PUBSUB_TOPIC")
-	dataset := serverutils.MustGetEnvVar("CLOUD_HEALTH_DATASET_ID")
-	fhirStore := serverutils.MustGetEnvVar("CLOUD_HEALTH_FHIRSTORE_ID")
-	hsv, err := healthcare.NewService(ctx)
-	if err != nil {
-		log.Panicf("unable to initialize new Google Cloud Healthcare Service: %s", err)
-	}
+func NewFHIRRepository(ctx context.Context, hsv *healthcare.Service, projectID, datasetID, datasetLocation, fhirStoreID string) *Repository {
 	return &Repository{
 		healthcareService: hsv,
-		projectID:         project,
-		location:          DatasetLocation,
-		datasetID:         dataset,
-		fhirStoreID:       fhirStore,
+		projectID:         projectID,
+		location:          datasetLocation,
+		datasetID:         datasetID,
+		fhirStoreID:       fhirStoreID,
+		parent:            fmt.Sprintf("projects/%s/locations/%s", projectID, datasetLocation),
+		datasetName:       fmt.Sprintf("projects/%s/locations/%s/datasets/%s", projectID, datasetLocation, datasetID),
+		fhirStoreName:     fmt.Sprintf("projects/%s/locations/%s/datasets/%s/fhirStores/%s", projectID, datasetLocation, datasetID, fhirStoreID),
 	}
 }
 
 // CreateDataset creates a dataset and returns it's name
 func (fr Repository) CreateDataset() (*healthcare.Operation, error) {
 	fr.checkPreconditions()
 	datasetsService := fr.healthcareService.Projects.Locations.Datasets
-	parent := fmt.Sprintf("projects/%s/locations/%s", fr.projectID, fr.location)
-	resp, err := datasetsService.Create(parent, &healthcare.Dataset{}).DatasetId(fr.datasetID).Do()
+	resp, err := datasetsService.Create(fr.parent, &healthcare.Dataset{}).DatasetId(fr.datasetID).Do()
 	if err != nil {
 		return nil, fmt.Errorf("create Data Set: %w", err)
 	}
@@ -66,15 +62,14 @@ func (fr Repository) CreateDataset() (*healthcare.Operation, error) {
 func (fr Repository) GetDataset() (*healthcare.Dataset, error) {
 	fr.checkPreconditions()
 	datasetsService := fr.healthcareService.Projects.Locations.Datasets
-	name := fmt.Sprintf("projects/%s/locations/%s/datasets/%s", fr.projectID, fr.location, fr.datasetID)
-	resp, err := datasetsService.Get(name).Do()
+	resp, err := datasetsService.Get(fr.datasetName).Do()
 	if err != nil {
 		return nil, fmt.Errorf("get Data Set: %w", err)
 	}
 	return resp, nil
 }
 
-// CreateFHIRStore creates an FHIR store.
+// CreateFHIRStore creates a FHIR store.
 func (fr Repository) CreateFHIRStore() (*healthcare.FhirStore, error) {
 	fr.checkPreconditions()
 	storesService := fr.healthcareService.Projects.Locations.Datasets.FhirStores
@@ -84,8 +79,7 @@ func (fr Repository) CreateFHIRStore() (*healthcare.FhirStore, error) {
 		EnableUpdateCreate:          true,
 		Version:                     "R4",
 	}
-	parent := fmt.Sprintf("projects/%s/locations/%s/datasets/%s", fr.projectID, fr.location, fr.datasetID)
-	resp, err := storesService.Create(parent, store).FhirStoreId(fr.fhirStoreID).Do()
+	resp, err := storesService.Create(fr.datasetName, store).FhirStoreId(fr.fhirStoreID).Do()
 	if err != nil {
 		return nil, fmt.Errorf("create FHIR Store: %w", err)
 	}
@@ -96,10 +90,7 @@ func (fr Repository) CreateFHIRStore() (*healthcare.FhirStore, error) {
 func (fr Repository) GetFHIRStore() (*healthcare.FhirStore, error) {
 	fr.checkPreconditions()
 	storesService := fr.healthcareService.Projects.Locations.Datasets.FhirStores
-	name := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s",
-		fr.projectID, fr.location, fr.datasetID, fr.fhirStoreID)
-	store, err := storesService.Get(name).Do()
+	store, err := storesService.Get(fr.fhirStoreName).Do()
 	if err != nil {
 		return nil, fmt.Errorf("get FHIR Store: %w", err)
 	}
@@ -148,12 +139,7 @@ func (fr Repository) CreateFHIRResource(resourceType string, payload map[string]
 		return nil, fmt.Errorf("json.Encode: %w", err)
 	}
 
-	parent := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s",
-		fr.projectID, fr.location, fr.datasetID, fr.fhirStoreID)
-	call := fhirService.Create(
-		parent, resourceType, bytes.NewReader(jsonPayload))
-
+	call := fhirService.Create(fr.fhirStoreName, resourceType, bytes.NewReader(jsonPayload))
 	call.Header().Set("Content-Type", "application/fhir+json;charset=utf-8")
 	resp, err := call.Do()
 	if err != nil {
@@ -183,11 +169,8 @@ func (fr Repository) DeleteFHIRResource(resourceType, fhirResourceID string) ([]
 	fr.checkPreconditions()
 
 	fhirService := fr.healthcareService.Projects.Locations.Datasets.FhirStores.Fhir
-	name := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s/fhir/%s/%s",
-		fr.projectID, fr.location, fr.datasetID, fr.fhirStoreID,
-		resourceType, fhirResourceID)
-	resp, err := fhirService.Delete(name).Do()
+	fhirResource := fmt.Sprintf("%s/fhir/%s/%s", fr.fhirStoreName, resourceType, fhirResourceID)
+	resp, err := fhirService.Delete(fhirResource).Do()
 	if err != nil {
 		return nil, fmt.Errorf("delete: %w", err)
 	}
@@ -229,12 +212,8 @@ func (fr Repository) PatchFHIRResource(
 	if err != nil {
 		return nil, fmt.Errorf("json.Encode: %w", err)
 	}
-	name := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s/fhir/%s/%s",
-		fr.projectID, fr.location, fr.datasetID, fr.fhirStoreID,
-		resourceType, fhirResourceID)
-
-	call := fhirService.Patch(name, bytes.NewReader(jsonPayload))
+	fhirResource := fmt.Sprintf("%s/fhir/%s/%s", fr.fhirStoreName, resourceType, fhirResourceID)
+	call := fhirService.Patch(fhirResource, bytes.NewReader(jsonPayload))
 	call.Header().Set("Content-Type", "application/json-patch+json")
 	resp, err := call.Do()
 	if err != nil {
@@ -270,11 +249,8 @@ func (fr Repository) UpdateFHIRResource(
 	if serverutils.IsDebug() {
 		log.Printf("FHIR Update payload: %s", string(jsonPayload))
 	}
-	name := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s/fhir/%s/%s",
-		fr.projectID, fr.location, fr.datasetID, fr.fhirStoreID,
-		resourceType, fhirResourceID)
-	call := fhirService.Update(name, bytes.NewReader(jsonPayload))
+	fhirResource := fmt.Sprintf("%s/fhir/%s/%s", fr.fhirStoreName, resourceType, fhirResourceID)
+	call := fhirService.Update(fhirResource, bytes.NewReader(jsonPayload))
 	call.Header().Set("Content-Type", "application/fhir+json;charset=utf-8")
 	resp, err := call.Do()
 	if err != nil {
@@ -298,16 +274,8 @@ func (fr Repository) UpdateFHIRResource(
 // patient compartment.
 func (fr Repository) GetFHIRPatientAllData(fhirResourceID string) ([]byte, error) {
 	fhirService := fr.healthcareService.Projects.Locations.Datasets.FhirStores.Fhir
-	name := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s/fhir/Patient/%s",
-		fr.projectID,
-		fr.location,
-		fr.datasetID,
-		fr.fhirStoreID,
-		fhirResourceID,
-	)
-
-	resp, err := fhirService.PatientEverything(name).Do()
+	patientResource := fmt.Sprintf("%s/fhir/Patient/%s", fr.fhirStoreName, fhirResourceID)
+	resp, err := fhirService.PatientEverything(patientResource).Do()
 	if err != nil {
 		return nil, fmt.Errorf("PatientAllData: %w", err)
 	}
@@ -332,11 +300,8 @@ func (fr Repository) GetFHIRPatientAllData(fhirResourceID string) ([]byte, error
 func (fr Repository) GetFHIRResource(resourceType, fhirResourceID string) ([]byte, error) {
 	fr.checkPreconditions()
 	fhirService := fr.healthcareService.Projects.Locations.Datasets.FhirStores.Fhir
-	name := fmt.Sprintf(
-		"projects/%s/locations/%s/datasets/%s/fhirStores/%s/fhir/%s/%s",
-		fr.projectID, fr.location, fr.datasetID, fr.fhirStoreID,
-		resourceType, fhirResourceID)
-	call := fhirService.Read(name)
+	fhirResource := fmt.Sprintf("%s/fhir/%s/%s", fr.fhirStoreName, resourceType, fhirResourceID)
+	call := fhirService.Read(fhirResource)
 	call.Header().Set("Content-Type", "application/fhir+json;charset=utf-8")
 	resp, err := call.Do()
 	if err != nil {