msbukal commented on a change in pull request #15936:
URL: https://github.com/apache/beam/pull/15936#discussion_r756339041
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java
##########
@@ -1339,13 +1353,29 @@ public void importBatch(FinishBundleContext context)
throws IOException {
this.fhirStore = fhirStore;
}
- /**
- * Instantiates a new Execute bundles.
- *
- * @param fhirStore the fhir store
- */
- ExecuteBundles(String fhirStore) {
- this.fhirStore = StaticValueProvider.of(fhirStore);
+ @Override
+ ValueProvider<String> getFhirStore() {
+ return null;
+ }
+
+ @Override
+ WriteMethod getWriteMethod() {
+ return WriteMethod.EXECUTE_BUNDLE;
+ }
+
+ @Override
+ Optional<ContentStructure> getContentStructure() {
+ return Optional.empty();
+ }
+
+ @Override
+ Optional<ValueProvider<String>> getImportGcsTempPath() {
+ return Optional.empty();
+ }
+
+ @Override
+ Optional<ValueProvider<String>> getImportGcsDeadLetterPath() {
+ return Optional.empty();
Review comment:
I'm not sure what you mean, these methods are only here because I made
ExecuteBundles implement FhirIO.Write, which requires them.
##########
File path:
sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.java
##########
@@ -0,0 +1,237 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.beam.sdk.io.gcp.healthcare;
+
+import static org.apache.beam.sdk.io.gcp.healthcare.FhirIO.BASE_METRIC_PREFIX;
+
+import com.google.auto.value.AutoValue;
+import com.google.gson.JsonArray;
+import java.io.IOException;
+import java.io.Serializable;
+import java.time.Instant;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.NoSuchElementException;
+import org.apache.beam.sdk.Pipeline;
+import org.apache.beam.sdk.coders.StringUtf8Coder;
+import
org.apache.beam.sdk.io.gcp.healthcare.FhirIOPatientEverything.PatientEverythingParameter;
+import
org.apache.beam.sdk.io.gcp.healthcare.HttpHealthcareApiClient.FhirResourcePagesIterator;
+import org.apache.beam.sdk.metrics.Counter;
+import org.apache.beam.sdk.metrics.Distribution;
+import org.apache.beam.sdk.metrics.Metrics;
+import org.apache.beam.sdk.schemas.AutoValueSchema;
+import org.apache.beam.sdk.schemas.annotations.DefaultSchema;
+import org.apache.beam.sdk.transforms.DoFn;
+import org.apache.beam.sdk.transforms.PTransform;
+import org.apache.beam.sdk.transforms.ParDo;
+import org.apache.beam.sdk.values.PCollection;
+import org.apache.beam.sdk.values.PCollectionTuple;
+import org.apache.beam.sdk.values.PInput;
+import org.apache.beam.sdk.values.POutput;
+import org.apache.beam.sdk.values.PValue;
+import org.apache.beam.sdk.values.TupleTag;
+import org.apache.beam.sdk.values.TupleTagList;
+import
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Throwables;
+import
org.apache.beam.vendor.guava.v26_0_jre.com.google.common.collect.ImmutableMap;
+import org.checkerframework.checker.nullness.qual.Nullable;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/** The type FhirIOPatientEverything for querying a FHIR Patient resource's
compartment. * */
+public class FhirIOPatientEverything
+ extends PTransform<PCollection<PatientEverythingParameter>,
FhirIOPatientEverything.Result> {
+
+ /** The tag for the main output of FHIR Resources from a
GetPatientEverything request. */
+ public static final TupleTag<JsonArray> OUT = new TupleTag<JsonArray>() {};
+ /** The tag for the deadletter output of FHIR Resources from a
GetPatientEverything request. */
+ public static final TupleTag<HealthcareIOError<String>> DEAD_LETTER =
+ new TupleTag<HealthcareIOError<String>>() {};
+
+ /**
+ * PatientEverythingParameter defines required attributes for a FHIR
GetPatientEverything request
+ * in {@link FhirIOPatientEverything}. *
+ */
+ @DefaultSchema(AutoValueSchema.class)
+ @AutoValue
+ public abstract static class PatientEverythingParameter implements
Serializable {
+
+ /**
+ * FHIR Patient resource name in the format of
+ *
projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}.
+ */
+ abstract String getResourceName();
+ /** Optional filters for the request, eg. start, end, _type, _since,
_count */
+ abstract @Nullable Map<String, String> getFilters();
+
+ static Builder builder() {
+ return new
AutoValue_FhirIOPatientEverything_PatientEverythingParameter.Builder();
+ }
+
+ @AutoValue.Builder
+ abstract static class Builder {
+ abstract Builder setResourceName(String resourceName);
+
+ abstract Builder setFilters(Map<String, String> query);
+
+ abstract PatientEverythingParameter build();
+ }
+ }
+
+ /** The Result for a {@link FhirIOPatientEverything} request. */
+ public static class Result implements POutput, PInput {
+
+ private final PCollection<JsonArray> patientCompartments;
+ private final PCollection<HealthcareIOError<String>> failedReads;
+
+ PCollectionTuple pct;
+
+ /**
+ * Create FhirIOPatientEverything.Result form PCollectionTuple with OUT
and DEAD_LETTER tags.
+ *
+ * @param pct the pct
+ * @return the patient everything result
+ * @throws IllegalArgumentException the illegal argument exception
+ */
+ static Result of(PCollectionTuple pct) throws IllegalArgumentException {
+ if (pct.has(OUT) && pct.has(DEAD_LETTER)) {
+ return new Result(pct);
+ } else {
+ throw new IllegalArgumentException(
+ "The PCollection tuple must have the FhirIOPatientEverything.OUT "
+ + "and FhirIOPatientEverything.DEAD_LETTER tuple tags");
+ }
+ }
+
+ private Result(PCollectionTuple pct) {
+ this.pct = pct;
+ this.patientCompartments = pct.get(OUT).setCoder(JsonArrayCoder.of());
+ this.failedReads =
+
pct.get(DEAD_LETTER).setCoder(HealthcareIOErrorCoder.of(StringUtf8Coder.of()));
+ }
+
+ /**
+ * Gets failed reads.
+ *
+ * @return the failed reads
+ */
+ public PCollection<HealthcareIOError<String>> getFailedReads() {
+ return failedReads;
+ }
+
+ /**
+ * Gets the patient compartment responses for GetPatientEverything
requests.
+ *
+ * @return the read patient compartments
+ */
+ public PCollection<JsonArray> getPatientCompartments() {
+ return patientCompartments;
+ }
+
+ @Override
+ public Pipeline getPipeline() {
+ return this.pct.getPipeline();
+ }
+
+ @Override
+ public Map<TupleTag<?>, PValue> expand() {
Review comment:
Sorry... isn't this what I'm doing? The return type of the
FhirIOPatientEverything PTransform is Result, and there is the methods
getFailedReads and getPatientCompartments, but the type POutput has to
implement `expand`, like all the other .Result methods in FhirIO?
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