msbukal commented on a change in pull request #15936: URL: https://github.com/apache/beam/pull/15936#discussion_r753547920
########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.java ########## @@ -0,0 +1,317 @@ +/* + * 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.gson.JsonArray; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.io.Serializable; +import java.time.Instant; +import java.util.HashMap; +import java.util.Map; +import java.util.NoSuchElementException; +import java.util.Objects; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.coders.CustomCoder; +import org.apache.beam.sdk.coders.DefaultCoder; +import org.apache.beam.sdk.coders.MapCoder; +import org.apache.beam.sdk.coders.NullableCoder; +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.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}. * + */ + @DefaultCoder(PatientEverythingParameterCoder.class) + public static class PatientEverythingParameter implements Serializable { + + /** + * FHIR Patient resource name in the format of + * projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + */ + private final String resourceName; + /** Optional filters for the request, eg. start, end, _type, _since, _count */ + private final @Nullable Map<String, String> filters; + + PatientEverythingParameter(String resourceName, @Nullable Map<String, String> filters) { + this.resourceName = resourceName; + this.filters = filters; + } + + /** + * Creates a PatientEverythingParameter. + * + * @param resourceName The FHIR Patient resource name in the format of + * projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + * @return the PatientEverythingParameter + */ + public static PatientEverythingParameter of(String resourceName) { + return new PatientEverythingParameter(resourceName, null); + } + + /** + * Creates a PatientEverythingParameter. + * + * @param resourceName The FHIR Patient resource name in the format of + * projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + * @param filters Optional filters for the request. + * @return the PatientEverythingParameter + */ + public static PatientEverythingParameter of( + String resourceName, @Nullable Map<String, String> filters) { + return new PatientEverythingParameter(resourceName, filters); + } + + public String getResourceName() { + return resourceName; + } + + public @Nullable Map<String, String> getFilters() { + return filters; + } + + @Override + public boolean equals(@Nullable Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + PatientEverythingParameter that = (PatientEverythingParameter) o; + return Objects.equals(resourceName, that.getResourceName()) + && Objects.equals(filters, that.getFilters()); + } + + @Override + public int hashCode() { + return Objects.hash(resourceName, filters); + } + + @Override + public String toString() { + return String.format( + "FhirIOPatientEverything.Parameter{resourcePath='%s', filters='%s'}'", + resourceName, filters); + } + } + + /** PatientEverythingParameterCoder is a coder for {@link PatientEverythingParameter}. */ + public static class PatientEverythingParameterCoder + extends CustomCoder<PatientEverythingParameter> { + + private static final NullableCoder<String> STRING_CODER = + NullableCoder.of(StringUtf8Coder.of()); + private static final NullableCoder<Map<String, String>> MAP_CODER = + NullableCoder.of(MapCoder.of(StringUtf8Coder.of(), StringUtf8Coder.of())); + + public static PatientEverythingParameterCoder of() { + return new PatientEverythingParameterCoder(); + } + + @Override + public void encode(PatientEverythingParameter value, OutputStream outStream) + throws IOException { + STRING_CODER.encode(value.getResourceName(), outStream); + MAP_CODER.encode(value.getFilters(), outStream); + } + + @Override + public PatientEverythingParameter decode(InputStream inStream) throws IOException { + String resourceName = STRING_CODER.decode(inStream); + Map<String, String> queries = MAP_CODER.decode(inStream); + return PatientEverythingParameter.of(resourceName, queries); + } + } + + /** 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() { + return ImmutableMap.of(OUT, patientCompartments, DEAD_LETTER, failedReads); + } + + @Override + public void finishSpecifyingOutput( + String transformName, PInput input, PTransform<?, ?> transform) {} + } + + @Override + public Result expand(PCollection<PatientEverythingParameter> input) { + PCollectionTuple results = + input.apply( + "GetPatientEverything", + ParDo.of(new GetPatientEverythingFn()) + .withOutputTags(OUT, TupleTagList.of(DEAD_LETTER))); + return new Result(results); + } + + /** GetPatientEverythingFn executes a GetPatientEverything request. */ + static class GetPatientEverythingFn extends DoFn<PatientEverythingParameter, JsonArray> { + + private static final Counter GET_PATIENT_EVERYTHING_ERROR_COUNT = + Metrics.counter( + GetPatientEverythingFn.class, + BASE_METRIC_PREFIX + "get_patient_everything_error_count"); + private static final Counter GET_PATIENT_EVERYTHING_SUCCESS_COUNT = + Metrics.counter( + GetPatientEverythingFn.class, + BASE_METRIC_PREFIX + "get_patient_everything_success_count"); + private static final Distribution GET_PATIENT_EVERYTHING_LATENCY_MS = + Metrics.distribution( + GetPatientEverythingFn.class, BASE_METRIC_PREFIX + "get_patient_everything_latency_ms"); + private static final Logger LOG = LoggerFactory.getLogger(GetPatientEverythingFn.class); + + @SuppressWarnings("initialization.fields.uninitialized") + private HealthcareApiClient client; + + /** + * Instantiate healthcare client. + * + * @throws IOException the io exception + */ + @Setup + public void instantiateHealthcareClient() throws IOException { + this.client = new HttpHealthcareApiClient(); + } + + @ProcessElement + public void processElement(ProcessContext context) { + PatientEverythingParameter patientEverythingParameter = context.element(); + try { + context.output( + getPatientEverything( + patientEverythingParameter.getResourceName(), + patientEverythingParameter.getFilters())); + } catch (IllegalArgumentException | NoSuchElementException e) { Review comment: Yes, that's what I believe. ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIO.java ########## @@ -94,20 +96,36 @@ * * <h3>Reading</h3> * - * <p>FHIR resources can be read with {@link FhirIO.Read}, which supports use cases where you have - * a ${@link PCollection} of message IDs. This is appropriate for reading the Fhir notifications - * from a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases where you have a - * manually prepared list of messages that you need to process (e.g. in a text file read with {@link + * <p>FHIR resources can be read with {@link FhirIO.Read}, which supports use cases where you have a + * ${@link PCollection} of FHIR resource names in the format of projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + * This is appropriate for reading the Fhir notifications from + * a Pub/Sub subscription with {@link PubsubIO#readStrings()} or in cases where you have a manually + * prepared list of resources that you need to process (e.g. in a text file read with {@link * org.apache.beam.sdk.io.TextIO}*) . * - * <p>Fetch Resource contents from Fhir Store based on the {@link PCollection} of message ID - * strings {@link FhirIO.Read.Result} where one can call {@link Read.Result#getResources()} to - * retrieve a {@link PCollection} containing the successfully fetched {@link String}s and/or {@link - * FhirIO.Read.Result#getFailedReads()}* to retrieve a {@link PCollection} of {@link - * HealthcareIOError}* containing the resource ID that could not be fetched and the exception as a + * <<<<<<< HEAD Review comment: Whoops, missed these somehow because they didn't cause runtime errors haha. ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.java ########## @@ -0,0 +1,317 @@ +/* + * 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.gson.JsonArray; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.io.Serializable; +import java.time.Instant; +import java.util.HashMap; +import java.util.Map; +import java.util.NoSuchElementException; +import java.util.Objects; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.coders.CustomCoder; +import org.apache.beam.sdk.coders.DefaultCoder; +import org.apache.beam.sdk.coders.MapCoder; +import org.apache.beam.sdk.coders.NullableCoder; +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.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}. * + */ + @DefaultCoder(PatientEverythingParameterCoder.class) Review comment: Done, I made them AutoValue! ########## File path: sdks/java/io/google-cloud-platform/src/main/java/org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.java ########## @@ -0,0 +1,317 @@ +/* + * 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.gson.JsonArray; +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; +import java.io.Serializable; +import java.time.Instant; +import java.util.HashMap; +import java.util.Map; +import java.util.NoSuchElementException; +import java.util.Objects; +import org.apache.beam.sdk.Pipeline; +import org.apache.beam.sdk.coders.CustomCoder; +import org.apache.beam.sdk.coders.DefaultCoder; +import org.apache.beam.sdk.coders.MapCoder; +import org.apache.beam.sdk.coders.NullableCoder; +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.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}. * + */ + @DefaultCoder(PatientEverythingParameterCoder.class) + public static class PatientEverythingParameter implements Serializable { + + /** + * FHIR Patient resource name in the format of + * projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + */ + private final String resourceName; + /** Optional filters for the request, eg. start, end, _type, _since, _count */ + private final @Nullable Map<String, String> filters; + + PatientEverythingParameter(String resourceName, @Nullable Map<String, String> filters) { + this.resourceName = resourceName; + this.filters = filters; + } + + /** + * Creates a PatientEverythingParameter. + * + * @param resourceName The FHIR Patient resource name in the format of + * projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + * @return the PatientEverythingParameter + */ + public static PatientEverythingParameter of(String resourceName) { + return new PatientEverythingParameter(resourceName, null); + } + + /** + * Creates a PatientEverythingParameter. + * + * @param resourceName The FHIR Patient resource name in the format of + * projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. + * @param filters Optional filters for the request. + * @return the PatientEverythingParameter + */ + public static PatientEverythingParameter of( + String resourceName, @Nullable Map<String, String> filters) { + return new PatientEverythingParameter(resourceName, filters); + } + + public String getResourceName() { + return resourceName; + } + + public @Nullable Map<String, String> getFilters() { + return filters; + } + + @Override + public boolean equals(@Nullable Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + PatientEverythingParameter that = (PatientEverythingParameter) o; + return Objects.equals(resourceName, that.getResourceName()) + && Objects.equals(filters, that.getFilters()); + } + + @Override + public int hashCode() { + return Objects.hash(resourceName, filters); + } + + @Override + public String toString() { + return String.format( + "FhirIOPatientEverything.Parameter{resourcePath='%s', filters='%s'}'", + resourceName, filters); + } + } + + /** PatientEverythingParameterCoder is a coder for {@link PatientEverythingParameter}. */ + public static class PatientEverythingParameterCoder + extends CustomCoder<PatientEverythingParameter> { + + private static final NullableCoder<String> STRING_CODER = + NullableCoder.of(StringUtf8Coder.of()); + private static final NullableCoder<Map<String, String>> MAP_CODER = + NullableCoder.of(MapCoder.of(StringUtf8Coder.of(), StringUtf8Coder.of())); + + public static PatientEverythingParameterCoder of() { + return new PatientEverythingParameterCoder(); + } + + @Override + public void encode(PatientEverythingParameter value, OutputStream outStream) + throws IOException { + STRING_CODER.encode(value.getResourceName(), outStream); + MAP_CODER.encode(value.getFilters(), outStream); + } + + @Override + public PatientEverythingParameter decode(InputStream inStream) throws IOException { + String resourceName = STRING_CODER.decode(inStream); + Map<String, String> queries = MAP_CODER.decode(inStream); + return PatientEverythingParameter.of(resourceName, queries); + } + } + + /** 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() { + return ImmutableMap.of(OUT, patientCompartments, DEAD_LETTER, failedReads); + } + + @Override + public void finishSpecifyingOutput( + String transformName, PInput input, PTransform<?, ?> transform) {} + } + + @Override + public Result expand(PCollection<PatientEverythingParameter> input) { + PCollectionTuple results = + input.apply( + "GetPatientEverything", + ParDo.of(new GetPatientEverythingFn()) + .withOutputTags(OUT, TupleTagList.of(DEAD_LETTER))); + return new Result(results); + } + + /** GetPatientEverythingFn executes a GetPatientEverything request. */ + static class GetPatientEverythingFn extends DoFn<PatientEverythingParameter, JsonArray> { + + private static final Counter GET_PATIENT_EVERYTHING_ERROR_COUNT = + Metrics.counter( + GetPatientEverythingFn.class, + BASE_METRIC_PREFIX + "get_patient_everything_error_count"); + private static final Counter GET_PATIENT_EVERYTHING_SUCCESS_COUNT = + Metrics.counter( + GetPatientEverythingFn.class, + BASE_METRIC_PREFIX + "get_patient_everything_success_count"); + private static final Distribution GET_PATIENT_EVERYTHING_LATENCY_MS = + Metrics.distribution( + GetPatientEverythingFn.class, BASE_METRIC_PREFIX + "get_patient_everything_latency_ms"); + private static final Logger LOG = LoggerFactory.getLogger(GetPatientEverythingFn.class); + + @SuppressWarnings("initialization.fields.uninitialized") + private HealthcareApiClient client; + + /** + * Instantiate healthcare client. + * + * @throws IOException the io exception + */ + @Setup + public void instantiateHealthcareClient() throws IOException { + this.client = new HttpHealthcareApiClient(); + } + + @ProcessElement + public void processElement(ProcessContext context) { + PatientEverythingParameter patientEverythingParameter = context.element(); + try { + context.output( Review comment: Will follow up for this. -- This is an automated message from the Apache Git Service. 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