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