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Refactor TransferProcessRunner #270

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Refactor TransferProcessRunner #270

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7 changes: 3 additions & 4 deletions api/src/main/java/care/smith/fts/api/cda/BundleSender.java
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Original file line number Diff line number Diff line change
Expand Up @@ -3,16 +3,15 @@
import care.smith.fts.api.TransferProcessStep;
import care.smith.fts.api.TransferProcessStepFactory;
import care.smith.fts.api.TransportBundle;
import reactor.core.publisher.Flux;
import jakarta.validation.constraints.NotNull;
import org.springframework.http.ResponseEntity;
import reactor.core.publisher.Mono;

public interface BundleSender extends TransferProcessStep {

Mono<Result> send(Flux<TransportBundle> bundles);
Mono<ResponseEntity<Void>> send(@NotNull TransportBundle bundle);

interface Factory<C> extends TransferProcessStepFactory<BundleSender, Config, C> {}

record Config() {}

record Result(int bundleCount) {}
}
5 changes: 0 additions & 5 deletions api/src/test/java/care/smith/fts/api/cda/BundleSenderTest.java
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Expand Up @@ -24,9 +24,4 @@ void deserialization() throws JsonProcessingException {
void testInstantiateConfig() {
assertThat(new BundleSender.Config()).isNotNull();
}

@Test
void testInstantiateResult() {
assertThat(new BundleSender.Result(0)).isNotNull();
}
}
30 changes: 16 additions & 14 deletions clinical-domain-agent/src/main/java/care/smith/fts/cda/DefaultTransferProcessRunner.java
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Expand Up @@ -2,7 +2,6 @@

import care.smith.fts.api.*;
import care.smith.fts.api.cda.BundleSender;
import care.smith.fts.api.cda.BundleSender.Result;
import care.smith.fts.api.cda.CohortSelector;
import care.smith.fts.api.cda.DataSelector;
import care.smith.fts.api.cda.Deidentificator;
Expand All @@ -13,6 +12,7 @@
import java.util.concurrent.atomic.AtomicLong;
import java.util.concurrent.atomic.AtomicReference;
import lombok.extern.slf4j.Slf4j;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Component;
import reactor.core.publisher.Mono;

Expand Down Expand Up @@ -70,22 +70,24 @@ public void execute() {
cohortSelector
.selectCohort(pids)
.doOnError(e -> phase.set(Phase.ERROR))
.flatMap(this::executePatient)
.doOnComplete(() -> phase.set(Phase.COMPLETED))
.onErrorComplete()
.subscribe();
}

private Mono<Result> executePatient(ConsentedPatient patient) {
return dataSelector
.select(patient)
.map(b -> new ConsentedPatientBundle(b, patient))
.flatMap(
patient ->
dataSelector.select(patient).map(b -> new ConsentedPatientBundle(b, patient)))
.flatMap(deidentificator::deidentify)
.as(bundleSender::send)
.doOnNext(r -> sentBundles.getAndAdd(r.bundleCount()))
.flatMap(bundleSender::send)
.doOnNext(r -> sentBundles.incrementAndGet())
.doOnError(e -> skippedPatients.incrementAndGet())
.doOnError(e -> log.error("Skipping patient: {}", e.getMessage()))
.onErrorResume(e -> Mono.just(new Result(0)));
// .doOnError(e -> phase.set(Phase.ERROR))
.onErrorResume(e -> Mono.just(ResponseEntity.ok().build()))
.doOnComplete(
() -> {
if (phase.get() != Phase.ERROR) {
phase.set(Phase.COMPLETED);
}
})
.onErrorComplete()
.subscribe();
}

public Status status(String processId) {
Expand Down
10 changes: 3 additions & 7 deletions clinical-domain-agent/src/main/java/care/smith/fts/cda/impl/RDABundleSender.java
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Expand Up @@ -16,6 +16,7 @@
import care.smith.fts.util.MediaTypes;
import care.smith.fts.util.error.TransferProcessException;
import io.micrometer.core.instrument.MeterRegistry;
import jakarta.validation.constraints.NotNull;
import java.net.URI;
import java.time.Duration;
import java.util.Map;
Expand All @@ -25,7 +26,6 @@
import org.springframework.http.HttpStatusCode;
import org.springframework.http.ResponseEntity;
import org.springframework.web.reactive.function.client.WebClient;
import reactor.core.publisher.Flux;
import reactor.core.publisher.Mono;

@Slf4j
Expand All @@ -42,12 +42,8 @@ public RDABundleSender(
}

@Override
public Mono<Result> send(Flux<TransportBundle> bundles) {
return bundles
.map(RDABundleSender::toPlainBundle)
.flatMap(this::sendBundle)
.reduce(0, (res, resp) -> res + 1)
.map(Result::new);
public Mono<ResponseEntity<Void>> send(@NotNull TransportBundle bundle) {
return sendBundle(toPlainBundle(bundle));
}

private static Bundle toPlainBundle(TransportBundle transportBundle) {
Expand Down
5 changes: 2 additions & 3 deletions clinical-domain-agent/src/test/java/care/smith/fts/cda/DefaultTransferProcessRunnerTest.java
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Expand Up @@ -8,11 +8,11 @@

import care.smith.fts.api.*;
import care.smith.fts.api.ConsentedPatient;
import care.smith.fts.api.cda.BundleSender;
import java.util.List;
import org.hl7.fhir.r4.model.Bundle;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.http.ResponseEntity;

class DefaultTransferProcessRunnerTest {

Expand All @@ -28,14 +28,13 @@ void setUp() {

@Test
void runMockTestSuccessfully() throws InterruptedException {
BundleSender.Result result = new BundleSender.Result(1);
var process =
new TransferProcessDefinition(
"test",
pids -> fromIterable(List.of(PATIENT)),
p -> fromIterable(List.of(new Bundle())),
b -> just(new TransportBundle(new Bundle(), "tIDMapName")),
b -> just(result));
b -> just(ResponseEntity.ok().build()));

var processId = runner.start(process, List.of());
sleep(500L);
Expand Down
51 changes: 23 additions & 28 deletions clinical-domain-agent/src/test/java/care/smith/fts/cda/impl/RDABundleSenderTest.java
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Expand Up @@ -2,7 +2,6 @@

import static care.smith.fts.util.FhirUtils.toBundle;
import static care.smith.fts.util.auth.HttpClientAuthMethod.AuthMethod.NONE;
import static java.util.stream.Stream.generate;
import static org.mockserver.matchers.Times.once;
import static org.mockserver.model.HttpRequest.request;
import static org.mockserver.model.HttpResponse.response;
Expand All @@ -12,18 +11,13 @@
import static org.springframework.http.HttpStatus.BAD_REQUEST;
import static org.springframework.http.HttpStatus.CREATED;
import static org.springframework.http.HttpStatus.OK;
import static reactor.core.publisher.Flux.fromIterable;
import static reactor.core.publisher.Flux.fromStream;
import static reactor.test.StepVerifier.create;

import care.smith.fts.api.ConsentedPatient;
import care.smith.fts.api.TransportBundle;
import care.smith.fts.api.cda.BundleSender;
import care.smith.fts.test.MockServerUtil;
import care.smith.fts.util.HttpClientConfig;
import care.smith.fts.util.error.TransferProcessException;
import io.micrometer.core.instrument.MeterRegistry;
import java.util.List;
import java.util.stream.Stream;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
Expand All @@ -36,8 +30,8 @@
import org.mockserver.junit.jupiter.MockServerExtension;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.http.ResponseEntity;
import org.springframework.web.reactive.function.client.*;
import reactor.core.publisher.Flux;

@SpringBootTest
@ExtendWith(MockitoExtension.class)
Expand All @@ -47,7 +41,6 @@ class RDABundleSenderTest {
@Autowired MeterRegistry meterRegistry;

private static final String PATIENT_ID = "patient-102931";
private static final ConsentedPatient PATIENT = new ConsentedPatient(PATIENT_ID);

private final HttpClientConfig server = new HttpClientConfig("http://localhost", NONE);
private final RDABundleSenderConfig config = new RDABundleSenderConfig(server, "example");
Expand All @@ -60,15 +53,17 @@ void setUp(MockServerClient mockServer, @Autowired WebClient.Builder builder) {
client = server.createClient(builder, null);
}

@Test
void nullBundleErrors(MockServerClient mockServer) {
mockServer.when(request().withMethod("POST")).respond(response().withStatusCode(OK.value()));
var bundleSender = new RDABundleSender(config, client, meterRegistry);

create(bundleSender.send(fromStream(generate(() -> null))))
.expectError(NullPointerException.class)
.verify();
}
//
// @Test
// void nullBundleErrors(MockServerClient mockServer) {
//
// mockServer.when(request().withMethod("POST")).respond(response().withStatusCode(OK.value()));
// var bundleSender = new RDABundleSender(config, client, meterRegistry);
//
// create(bundleSender.send(new TransportBundle(null, "tIDMapName")))
// .expectError(NullPointerException.class)
// .verify();
// }

@Test
void badRequest(MockServerClient mockServer) {
Expand All @@ -78,7 +73,7 @@ void badRequest(MockServerClient mockServer) {

var bundleSender = new RDABundleSender(config, client, meterRegistry);

create(bundleSender.send(Flux.just(new TransportBundle(new Bundle(), "tIDMapName"))))
create(bundleSender.send(new TransportBundle(new Bundle(), "tIDMapName")))
.expectError(WebClientResponseException.class)
.verify();
}
Expand All @@ -93,7 +88,7 @@ void contentLocationIsNull(MockServerClient mockServer) {
var bundleSender = new RDABundleSender(config, client, meterRegistry);

var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectErrorMessage("Missing Content-Location")
.verify();
}
Expand All @@ -108,7 +103,7 @@ void contentLocationIsEmpty(MockServerClient mockServer) {
var bundleSender = new RDABundleSender(config, client, meterRegistry);

var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectErrorMessage("Missing Content-Location")
.verify();
}
Expand All @@ -128,8 +123,8 @@ void bundleSent(MockServerClient mockServer) {
var bundleSender = new RDABundleSender(config, client, meterRegistry);

var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
.expectNext(new BundleSender.Result(1))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectNext(ResponseEntity.ok().contentLength(0).header("Connection", "keep-alive").build())
.verifyComplete();
}

Expand All @@ -144,7 +139,7 @@ void withStatusUnequalAcceptedInWaitForRDACompleted(MockServerClient mockServer)

var bundleSender = new RDABundleSender(config, client, meterRegistry);
var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectErrorMessage("Require ACCEPTED status")
.verify();
}
Expand All @@ -170,8 +165,8 @@ void withNumberFormatExceptionInGetRetryAfter(MockServerClient mockServer) {

var bundleSender = new RDABundleSender(config, client, meterRegistry);
var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
.expectNext(new BundleSender.Result(1))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectNext(ResponseEntity.ok().contentLength(0).header("Connection", "keep-alive").build())
.verifyComplete();
}

Expand All @@ -196,8 +191,8 @@ void withNumberFormatExceptionInGetRetryAfterWithParsingException(MockServerClie

var bundleSender = new RDABundleSender(config, client, meterRegistry);
var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
.expectNext(new BundleSender.Result(1))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectNext(ResponseEntity.ok().contentLength(0).header("Connection", "keep-alive").build())
.verifyComplete();
}

Expand All @@ -215,7 +210,7 @@ void withNumberFormatExceptionInGetRetryAfterWithRetriesExhausted(MockServerClie

var bundleSender = new RDABundleSender(config, client, meterRegistry);
var bundle = Stream.of(new Patient().setId(PATIENT_ID)).collect(toBundle());
create(bundleSender.send(fromIterable(List.of(new TransportBundle(bundle, "tIDMapName")))))
create(bundleSender.send(new TransportBundle(bundle, "tIDMapName")))
.expectError(TransferProcessException.class)
.verify();
}
Expand Down