Merge pull request #52 from fastenhealth/resource_type_allow_list

adding support for a resource type allow list

Dockerfile

@@ -3,8 +3,8 @@ FROM golang:1.21
 WORKDIR /go/src/github.com/fastenhealth/fasten-sources
 COPY . .
 
-RUN go mod tidy && go mod vendor && go build -o /usr/bin/oauth_cli ./testutils/oauth_cli.go
+RUN go mod tidy && go mod vendor && go build -o /usr/bin/test-smart-client ./tools/test-smart-client/main.go
 
-CMD ["/usr/bin/oauth_cli"]
+CMD ["/usr/bin/test-smart-client"]
 
 EXPOSE 9999

clients/internal/base/base_client.go

@@ -34,8 +34,8 @@ type SourceClientBase struct {
 	EndpointDefinition *definitionsModels.LighthouseSourceDefinition
 	Headers            map[string]string
 
-	UsCoreResources []string
-	FhirVersion     string
+	ResourceTypesUsCore []string
+	FhirVersion         string
 
 	SourceClientOptions *models.SourceClientOptions
 
@@ -69,7 +69,7 @@ func NewBaseClient(env pkg.FastenLighthouseEnvType, ctx context.Context, globalL
 		Headers:            map[string]string{},
 
 		// https://build.fhir.org/ig/HL7/US-Core/
-		UsCoreResources: []string{
+		ResourceTypesUsCore: []string{
 			"AllergyIntolerance",
 			//"Binary",
 			"CarePlan",
@@ -113,8 +113,16 @@ func NewBaseClient(env pkg.FastenLighthouseEnvType, ctx context.Context, globalL
 	return client, nil
 }
 
-func (c *SourceClientBase) GetUsCoreResources() []string {
-	return c.UsCoreResources
+func (c *SourceClientBase) GetResourceTypesUsCore() []string {
+	return c.ResourceTypesUsCore
+}
+
+func (c *SourceClientBase) GetResourceTypesAllowList() []string {
+	if c.SourceClientOptions == nil {
+		return []string{}
+	} else {
+		return c.SourceClientOptions.ResourceTypesAllowList
+	}
 }
 
 func (c *SourceClientBase) GetSourceCredential() models.SourceCredential {

clients/internal/base/fhir401_client.go

@@ -198,7 +198,10 @@ func (c *SourceClientFHIR401) SyncAllByResourceName(db models.DatabaseRepository
 	}
 
 	//process any pending resources
-	lookupResourceReferences, syncErrors = c.ProcessPendingResources(db, &summary, lookupResourceReferences, syncErrors)
+	//if we have a populated whitelist, skip this -- we don't care about references to other resources, just the ones we queried. This is a naiive solution to prevent requesting unnecessary records. This should be improved.
+	if len(c.GetResourceTypesAllowList()) == 0 {
+		lookupResourceReferences, syncErrors = c.ProcessPendingResources(db, &summary, lookupResourceReferences, syncErrors)
+	}
 
 	checkpointErrorData := map[string]interface{}{}
 	if len(syncErrors) > 0 {
@@ -469,6 +472,11 @@ func (c *SourceClientFHIR401) ProcessResource(db models.DatabaseRepository, reso
 				c.Logger.Warnf("Skipping contained resource missing id: (%s/%s#%s index: %d)", currentResourceType, *currentResourceId, containedResourceType, cndx)
 				continue
 			}
+			if len(c.GetResourceTypesAllowList()) > 0 && !lo.Contains(c.GetResourceTypesAllowList(), containedResourceType) {
+				c.Logger.Warnf("Skipping contained resource not in allow list: (%s/%s#%s index: %d)", currentResourceType, *currentResourceId, containedResourceType, cndx)
+				continue
+			}
+
 			normalizedContainedResourceId := normalizeContainedResourceId(currentResourceType, *currentResourceId, *containedResourceId)
 
 			//generate a unique id for this contained resource by base64 url encoding this string

clients/internal/dynamic_client.go

@@ -68,9 +68,16 @@ func (c dynamicSourceClient) SyncAll(db models.DatabaseRepository) (models.Upser
 		//Operation-PatientEverything is not supported - https://build.fhir.org/operation-patient-everything.html
 		//Manually processing individual resources
 
-		supportedResources := c.GetUsCoreResources()
-		if c.EndpointDefinition.ClientSupportedResources != nil {
-			supportedResources = append(supportedResources, c.EndpointDefinition.ClientSupportedResources...)
+		var supportedResources []string
+		if len(c.GetResourceTypesAllowList()) > 0 {
+			supportedResources = c.GetResourceTypesAllowList()
+			supportedResources = append(supportedResources, "Patient") //always ensure the patient is included
+		} else {
+			//no override provided, attempt to sync all resources
+			supportedResources = c.GetResourceTypesUsCore()
+			if c.EndpointDefinition.ClientSupportedResources != nil {
+				supportedResources = append(supportedResources, c.EndpointDefinition.ClientSupportedResources...)
+			}
 		}
 		return c.SyncAllByResourceName(db, supportedResources)
 	} else if len(c.EndpointDefinition.CustomOpPatientEverything) > 0 {

clients/internal/dynamic_client_test.go

@@ -0,0 +1,14 @@
+package internal
+
+import (
+	"github.com/fastenhealth/fasten-sources/clients/models"
+	"github.com/stretchr/testify/require"
+	"testing"
+)
+
+func TestGetDynamicSourceClient_ImplementsInterface(t *testing.T) {
+	t.Parallel()
+
+	//assert
+	require.Implements(t, (*models.SourceClient)(nil), &dynamicSourceClient{}, "should implement the models.SourceClient interface")
+}

clients/internal/fasten/client_test.go

@@ -0,0 +1,14 @@
+package fasten
+
+import (
+	"github.com/fastenhealth/fasten-sources/clients/models"
+	"github.com/stretchr/testify/require"
+	"testing"
+)
+
+func TestGetSourceClientFasten_ImplementsInterface(t *testing.T) {
+	t.Parallel()
+
+	//assert
+	require.Implements(t, (*models.SourceClient)(nil), &FastenClient{}, "should implement the models.SourceClient interface")
+}

clients/internal/manual/client.go

@@ -45,6 +45,14 @@ func (m ManualClient) GetUsCoreResources() []string {
 	panic("implement me")
 }
 
+func (m ManualClient) GetResourceTypesUsCore() []string {
+	return []string{}
+}
+
+func (m ManualClient) GetResourceTypesAllowList() []string {
+	return []string{}
+}
+
 func (m ManualClient) SyncAllByResourceName(db models.DatabaseRepository, resourceNames []string) (models.UpsertSummary, error) {
 	//TODO implement me
 	panic("implement me")

clients/internal/manual/client_test.go

@@ -2,6 +2,7 @@ package manual
 
 import (
 	"context"
+	"github.com/fastenhealth/fasten-sources/clients/models"
 	mock_models "github.com/fastenhealth/fasten-sources/clients/models/mock"
 	"github.com/fastenhealth/fasten-sources/pkg"
 	"github.com/golang/mock/gomock"
@@ -11,6 +12,13 @@ import (
 	"testing"
 )
 
+func TestGetSourceClientManual_ImplementsInterface(t *testing.T) {
+	t.Parallel()
+
+	//assert
+	require.Implements(t, (*models.SourceClient)(nil), &ManualClient{}, "should implement the models.SourceClient interface")
+}
+
 func TestGetSourceClientManual_ExtractPatientId_Bundle(t *testing.T) {
 	t.Parallel()
 	//setup

clients/models/source_client.go

@@ -7,7 +7,8 @@ import (
 
 //go:generate mockgen -source=source_client.go -destination=mock/mock_source_client.go
 type SourceClient interface {
-	GetUsCoreResources() []string
+	GetResourceTypesUsCore() []string
+	GetResourceTypesAllowList() []string
 	GetRequest(resourceSubpath string, decodeModelPtr interface{}) (string, error)
 	GetResourceBundle(relativeResourcePath string) (interface{}, error)
 	SyncAll(db DatabaseRepository) (UpsertSummary, error)

clients/models/source_client_options.go

@@ -17,6 +17,8 @@ type SourceClientOptions struct {
 	RedirectURL  string
 	Scopes       []string
 
+	ResourceTypesAllowList []string //list of resource types that are allowed to be fetched from this source. Default empty (USCDI Core List)
+
 	SourceClientRefreshOptions []func(*SourceClientRefreshOptions)
 
 	Context context.Context
@@ -65,6 +67,12 @@ func WithScopes(scopes []string) func(*SourceClientOptions) {
 	}
 }
 
+func WithResourceTypeAllowList(resourceTypeAllowList []string) func(*SourceClientOptions) {
+	return func(s *SourceClientOptions) {
+		s.ResourceTypesAllowList = resourceTypeAllowList
+	}
+}
+
 func WithSourceClientRefreshOptions(options ...func(*SourceClientRefreshOptions)) func(*SourceClientOptions) {
 	return func(s *SourceClientOptions) {
 		s.SourceClientRefreshOptions = options