[GitHub] [beam] msbukal commented on a diff in pull request #22152: Add fhirio.Deidentify transform

[GitBox <gi...@apache.org>]

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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