msbukal commented on code in PR #22152:
URL: https://github.com/apache/beam/pull/22152#discussion_r914215980
##########
sdks/go/pkg/beam/io/fhirio/common.go:
##########
@@ -91,18 +98,61 @@ func (c *fhirStoreClientImpl) search(storePath,
resourceType string, queries map
}
searchRequest := &healthcare.SearchResourcesRequest{}
+ fhirService :=
c.healthcareService.Projects.Locations.Datasets.FhirStores.Fhir
+
if resourceType == "" {
- return c.fhirService.Search(storePath,
searchRequest).Do(queryParams...)
+ return fhirService.Search(storePath,
searchRequest).Do(queryParams...)
+ }
+ return fhirService.SearchType(storePath, resourceType,
searchRequest).Do(queryParams...)
+}
+
+func (c *fhirStoreClientImpl) deidentify(srcStorePath, dstStorePath string,
deidConfig *healthcare.DeidentifyConfig) (operationResults, error) {
+ deidRequest := &healthcare.DeidentifyFhirStoreRequest{
+ Config: deidConfig,
+ DestinationStore: dstStorePath,
+ }
+ operation, err :=
c.healthcareService.Projects.Locations.Datasets.FhirStores.Deidentify(srcStorePath,
deidRequest).Do()
+ if err != nil {
+ return operationResults{}, err
+ }
+ return c.waitTillCompleteAndCollectResults(operation)
+}
+
+func (c *fhirStoreClientImpl) waitTillCompleteAndCollectResults(operation
*healthcare.Operation) (operationResults, error) {
+ var err error
+ for !operation.Done {
+ time.Sleep(5 * time.Second)
Review Comment:
You should poll for longer between checking the operation - these operations
run for a while usually, so we're wasting time.
You can see a PR I did this in for Java:
https://github.com/apache/beam/pull/15921, looks like I chose 15 seconds so
that should be fine.
##########
sdks/go/pkg/beam/io/fhirio/utils_test.go:
##########
@@ -118,19 +127,23 @@ func (m *fakeReaderCloser) Read(b []byte) (int, error) {
return m.fakeRead(b)
}
-func validateCounter(pipelineResult beam.PipelineResult, expectedCounterName
string, expectedCount int) error {
- counterResults := pipelineResult.Metrics().AllMetrics().Counters()
- if len(counterResults) != 1 {
- return fmt.Errorf("counterResults got length %v, expected %v",
len(counterResults), 1)
+func validateCounter(t *testing.T, pipelineResult beam.PipelineResult,
expectedCounterName string, expectedCount int) {
+ t.Helper()
+
+ counterResults := pipelineResult.Metrics().Query(func(mr
beam.MetricResult) bool {
+ return mr.Name() == expectedCounterName
+ }).Counters()
+
+ if expectedCount == 0 && len(counterResults) == 0 {
+ return
}
- counterResult := counterResults[0]
- if counterResult.Name() != expectedCounterName {
- return fmt.Errorf("counterResult.Name() is '%v', expected
'%v'", counterResult.Name(), expectedCounterName)
+ if len(counterResults) != 1 {
+ t.Fatalf("counter %v got length %v, expected %v",
expectedCounterName, len(counterResults), 1)
Review Comment:
It looks like this error string should be something like `got %v counters
with name %v, expected 1`, correct? Am I understanding this? The error message
kind of looks like you're saying we got the wrong results for the counter.
##########
sdks/go/pkg/beam/io/fhirio/common.go:
##########
@@ -91,18 +98,61 @@ func (c *fhirStoreClientImpl) search(storePath,
resourceType string, queries map
}
searchRequest := &healthcare.SearchResourcesRequest{}
+ fhirService :=
c.healthcareService.Projects.Locations.Datasets.FhirStores.Fhir
+
if resourceType == "" {
- return c.fhirService.Search(storePath,
searchRequest).Do(queryParams...)
+ return fhirService.Search(storePath,
searchRequest).Do(queryParams...)
+ }
+ return fhirService.SearchType(storePath, resourceType,
searchRequest).Do(queryParams...)
+}
+
+func (c *fhirStoreClientImpl) deidentify(srcStorePath, dstStorePath string,
deidConfig *healthcare.DeidentifyConfig) (operationResults, error) {
+ deidRequest := &healthcare.DeidentifyFhirStoreRequest{
+ Config: deidConfig,
+ DestinationStore: dstStorePath,
+ }
+ operation, err :=
c.healthcareService.Projects.Locations.Datasets.FhirStores.Deidentify(srcStorePath,
deidRequest).Do()
+ if err != nil {
+ return operationResults{}, err
+ }
+ return c.waitTillCompleteAndCollectResults(operation)
+}
+
+func (c *fhirStoreClientImpl) waitTillCompleteAndCollectResults(operation
*healthcare.Operation) (operationResults, error) {
Review Comment:
nit till->til and wait->poll
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