trucleduc commented on a change in pull request #12721:
URL: https://github.com/apache/beam/pull/12721#discussion_r482969620
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -1297,4 +1362,67 @@ public void exportResourcesToGcs(ProcessContext context)
}
}
}
+
+ /** Deidentify FHIR resources from a FHIR store to a destination FHIR store
*/
+ public static class Deidentify extends PTransform<PBegin,
PCollection<String>> {
+ private final ValueProvider<String> sourceFhirStore;
+ private final ValueProvider<String> destinationFhirStore;
+ private final ValueProvider<DeidentifyConfig> deidConfig;
+
+ public Deidentify(
+ ValueProvider<String> sourceFhirStore,
+ ValueProvider<String> destinationFhirStore,
+ ValueProvider<DeidentifyConfig> deidConfig) {
+ this.sourceFhirStore = sourceFhirStore;
+ this.destinationFhirStore = destinationFhirStore;
+ this.deidConfig = deidConfig;
+ }
+
+ @Override
+ public PCollection<String> expand(PBegin input) {
+ return input
+ .getPipeline()
+ .apply(Create.ofProvider(sourceFhirStore, StringUtf8Coder.of()))
+ .apply(
+ "ScheduleDeidentifyFhirStoreOperations",
+ ParDo.of(new DeidentifyFn(destinationFhirStore, deidConfig)));
+ }
+
+ /** A function that schedules a deidentify operation and monitors the
status. */
+ public static class DeidentifyFn extends DoFn<String, String> {
+
+ private HealthcareApiClient client;
+ private final ValueProvider<String> destinationFhirStore;
+ private final String deidConfigJson;
+
+ public DeidentifyFn(
+ ValueProvider<String> destinationFhirStore,
ValueProvider<DeidentifyConfig> deidConfig) {
+ this.destinationFhirStore = destinationFhirStore;
+ Gson g = new Gson();
+ this.deidConfigJson = g.toJson(deidConfig.get());
+ }
+
+ @Setup
+ public void initClient() throws IOException {
+ this.client = new HttpHealthcareApiClient();
+ }
+
+ @ProcessElement
+ public void deidentify(ProcessContext context)
+ throws IOException, InterruptedException, HealthcareHttpException {
+ String sourceFhirStore = context.element();
+ String destinationFhirStore = this.destinationFhirStore.get();
+ Gson g = new Gson();
Review comment:
Gson class in also not serializable. So I reverted back to the original
version. Do you know what is the good way to do it? For me, I think Gson object
is not a big deal though as this transform is expected to operation at FHIR
store level, which is usually a few.
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