WIP Add oauth2 Client Credentials Flow

auth/README.md

@@ -0,0 +1 @@
+# Authn/Authz Util

auth/compose.yaml

@@ -0,0 +1,23 @@
+name: fts-auth
+
+services:
+  keycloak:
+    image: quay.io/keycloak/keycloak:25.0.6
+    command: [ "start-dev" ]
+    environment:
+      KEYCLOAK_ADMIN: admin
+      KEYCLOAK_ADMIN_PASSWORD: admin
+    ports:
+    - "8080:8080"
+    networks: [ "clinical-domain", "research-domain", "trust-center" ]
+
+networks:
+  clinical-domain:
+    external: true
+    name: fts-test_clinical-domain
+  research-domain:
+    external: true
+    name: fts-test_research-domain
+  trust-center:
+    external: true
+    name: fts-test_trust-center

clinical-domain-agent/application-auth:oauth2.yaml

@@ -0,0 +1,31 @@
+server:
+  port: 9090
+
+projects:
+  directory: "../.github/test/cd-agent/projects"
+
+security:
+  auth:
+    oauth2:
+      issuer: http://localhost:8080/realms/master
+
+spring:
+  security:
+    oauth2:
+      client:
+        registration:
+          agent:
+            authorizationGrantType: client_credentials
+            clientId: fts/cd-agent
+            clientSecret: eA4xj1zFxsVYZGdLah9KnkcmHYDBjojr
+            provider: keycloak
+        provider:
+          keycloak:
+            issuer-uri: http://localhost:8080/realms/master
+
+test:
+  webclient:
+    default:
+      auth:
+        oauth2:
+          registration: agent

clinical-domain-agent/src/main/java/care/smith/fts/cda/ClinicalDomainAgent.java

@@ -1,18 +1,10 @@
 package care.smith.fts.cda;
 
-import static java.time.Duration.ofSeconds;
-
-import ca.uhn.fhir.context.FhirContext;
-import care.smith.fts.util.CustomErrorHandler;
-import care.smith.fts.util.FhirCodecConfiguration;
-import care.smith.fts.util.MetricsConfig;
-import care.smith.fts.util.WebClientDefaults;
-import care.smith.fts.util.auth.HttpServerAuthConfig;
+import care.smith.fts.util.AgentConfiguration;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import java.net.http.HttpClient;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import lombok.extern.slf4j.Slf4j;
@@ -22,40 +14,17 @@
 import org.springframework.boot.context.properties.ConfigurationPropertiesScan;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Import;
-import org.springframework.context.annotation.Primary;
 
 @Slf4j
 @SpringBootApplication
 @ConfigurationPropertiesScan
-@Import({
-  WebClientDefaults.class,
-  FhirCodecConfiguration.class,
-  MetricsConfig.class,
-  HttpServerAuthConfig.class,
-  CustomErrorHandler.class,
-})
+@Import(AgentConfiguration.class)
 public class ClinicalDomainAgent {
 
   public static void main(String... args) {
     SpringApplication.run(ClinicalDomainAgent.class, args);
   }
 
-  @Bean
-  public FhirContext fhirContext() {
-    return FhirContext.forR4();
-  }
-
-  @Bean
-  public HttpClient httpClient() {
-    return HttpClient.newBuilder().connectTimeout(ofSeconds(10)).build();
-  }
-
-  @Bean
-  @Primary
-  public ObjectMapper defaultObjectMapper() {
-    return new ObjectMapper().registerModule(new JavaTimeModule());
-  }
-
   @Bean
   public ObjectMapper transferProcessObjectMapper() {
     return new ObjectMapper(new YAMLFactory())

clinical-domain-agent/src/main/java/care/smith/fts/cda/impl/DeidentifhirStepFactory.java

@@ -4,22 +4,19 @@
 import static java.util.Objects.requireNonNull;
 
 import care.smith.fts.api.cda.Deidentificator;
+import care.smith.fts.util.HttpClientFactory;
 import io.micrometer.core.instrument.MeterRegistry;
-import org.springframework.boot.autoconfigure.web.reactive.function.client.WebClientSsl;
 import org.springframework.stereotype.Component;
-import org.springframework.web.reactive.function.client.WebClient;
 
 @Component("deidentifhirDeidentificator")
 public class DeidentifhirStepFactory implements Deidentificator.Factory<DeidentifhirStepConfig> {
 
-  private final WebClient.Builder builder;
-  private final WebClientSsl ssl;
+  private final HttpClientFactory clientProvider;
   private final MeterRegistry meterRegistry;
 
   public DeidentifhirStepFactory(
-      WebClient.Builder builder, WebClientSsl ssl, MeterRegistry meterRegistry) {
-    this.builder = builder;
-    this.ssl = ssl;
+      HttpClientFactory clientProvider, MeterRegistry meterRegistry) {
+    this.clientProvider = clientProvider;
     this.meterRegistry = meterRegistry;
   }
 
@@ -31,7 +28,7 @@ public Class<DeidentifhirStepConfig> getConfigType() {
   @Override
   public Deidentificator create(
       Deidentificator.Config commonConfig, DeidentifhirStepConfig implConfig) {
-    var httpClient = implConfig.trustCenterAgent().server().createClient(builder, ssl);
+    var httpClient = clientProvider.createClient(implConfig.trustCenterAgent().server());
 
     return new DeidentifhirStep(
         httpClient,

clinical-domain-agent/src/main/java/care/smith/fts/cda/impl/EverythingDataSelectorFactory.java

@@ -2,10 +2,9 @@
 
 import care.smith.fts.api.cda.DataSelector;
 import care.smith.fts.cda.services.PatientIdResolver;
+import care.smith.fts.util.HttpClientFactory;
 import io.micrometer.core.instrument.MeterRegistry;
 import org.hl7.fhir.r4.model.IdType;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.web.reactive.function.client.WebClientSsl;
 import org.springframework.stereotype.Component;
 import org.springframework.web.reactive.function.client.WebClient;
 import reactor.core.publisher.Mono;
@@ -14,14 +13,12 @@
 public class EverythingDataSelectorFactory
     implements DataSelector.Factory<EverythingDataSelectorConfig> {
 
-  private final WebClient.Builder clientBuilder;
-  private final WebClientSsl ssl;
+  private final HttpClientFactory clientProvider;
   private final MeterRegistry meterRegistry;
 
   public EverythingDataSelectorFactory(
-      WebClient.Builder clientBuilder, WebClientSsl ssl, MeterRegistry meterRegistry) {
-    this.clientBuilder = clientBuilder;
-    this.ssl = ssl;
+      HttpClientFactory clientProvider, MeterRegistry meterRegistry) {
+    this.clientProvider = clientProvider;
     this.meterRegistry = meterRegistry;
   }
 
@@ -32,7 +29,7 @@ public Class<EverythingDataSelectorConfig> getConfigType() {
 
   @Override
   public DataSelector create(DataSelector.Config common, EverythingDataSelectorConfig config) {
-    var client = config.fhirServer().createClient(clientBuilder, ssl);
+    var client = clientProvider.createClient(config.fhirServer());
     PatientIdResolver resolver = createResolver(config, client);
     return new EverythingDataSelector(common, client, resolver, meterRegistry);
   }

clinical-domain-agent/src/main/java/care/smith/fts/cda/impl/RDABundleSenderFactory.java

@@ -1,22 +1,18 @@
 package care.smith.fts.cda.impl;
 
 import care.smith.fts.api.cda.BundleSender;
+import care.smith.fts.util.HttpClientFactory;
 import io.micrometer.core.instrument.MeterRegistry;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.web.reactive.function.client.WebClientSsl;
 import org.springframework.stereotype.Component;
-import org.springframework.web.reactive.function.client.WebClient;
 
 @Component("researchDomainAgentBundleSender")
 public class RDABundleSenderFactory implements BundleSender.Factory<RDABundleSenderConfig> {
 
-  private final WebClient.Builder builder;
-  private final WebClientSsl ssl;
+  private final HttpClientFactory clientProvider;
   private final MeterRegistry meterRegistry;
 
-  public RDABundleSenderFactory(WebClient.Builder builder, WebClientSsl ssl, MeterRegistry meterRegistry) {
-    this.builder = builder;
-    this.ssl = ssl;
+  public RDABundleSenderFactory(HttpClientFactory clientProvider, MeterRegistry meterRegistry) {
+    this.clientProvider = clientProvider;
     this.meterRegistry = meterRegistry;
   }
 
@@ -28,6 +24,6 @@ public Class<RDABundleSenderConfig> getConfigType() {
   @Override
   public BundleSender create(BundleSender.Config commonConfig, RDABundleSenderConfig implConfig) {
     return new RDABundleSender(
-        implConfig, implConfig.server().createClient(builder, ssl), meterRegistry);
+        implConfig, clientProvider.createClient(implConfig.server()), meterRegistry);
   }
 }

clinical-domain-agent/src/main/java/care/smith/fts/cda/impl/TCACohortSelectorFactory.java

@@ -3,26 +3,22 @@
 import static java.util.Objects.requireNonNull;
 
 import care.smith.fts.api.cda.CohortSelector;
+import care.smith.fts.util.HttpClientFactory;
 import io.micrometer.core.instrument.MeterRegistry;
 import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.web.reactive.function.client.WebClientSsl;
 import org.springframework.stereotype.Component;
-import org.springframework.web.reactive.function.client.WebClient;
 
 @Slf4j
 @Component("trustCenterAgentCohortSelector")
 public class TCACohortSelectorFactory implements CohortSelector.Factory<TCACohortSelectorConfig> {
-  private final WebClient.Builder clientBuilder;
-  private final WebClientSsl ssl;
+
+  private final HttpClientFactory clientProvider;
   private final MeterRegistry meterRegistry;
 
-  public TCACohortSelectorFactory(
-      WebClient.Builder clientBuilder, WebClientSsl ssl, MeterRegistry meterRegistry) {
-    this.ssl = ssl;
+  public TCACohortSelectorFactory(HttpClientFactory clientProvider, MeterRegistry meterRegistry) {
+    this.clientProvider = clientProvider;
     this.meterRegistry = meterRegistry;
-    log.info("Factory client {}", clientBuilder);
-    this.clientBuilder = requireNonNull(clientBuilder);
+    log.info("Factory client {}", clientProvider);
   }
 
   @Override
@@ -32,7 +28,7 @@ public Class<TCACohortSelectorConfig> getConfigType() {
 
   @Override
   public CohortSelector create(CohortSelector.Config ignored, TCACohortSelectorConfig config) {
-    var client = config.server().createClient(clientBuilder, ssl);
+    var client = clientProvider.createClient(config.server());
     log.info("Created Client {}", client);
     return new TCACohortSelector(config, client, meterRegistry);
   }

clinical-domain-agent/src/main/java/care/smith/fts/cda/rest/TransferProcessController.java

@@ -41,7 +41,7 @@ Mono<ResponseEntity<Object>> start(
       @RequestBody(required = false) List<String> pids) {
     var process = findProcess(project);
     if (process.isPresent()) {
-      log.debug("Running process: {}", process.get());
+      log.debug("Running process for project: {}", process.get().project());
 
       var id = processRunner.start(process.get(), Optional.ofNullable(pids).orElse(List.of()));
       var jobUri = generateJobUri(uriBuilder, id);

clinical-domain-agent/src/main/resources/application.yaml

@@ -1,3 +1,7 @@
+spring:
+  mustache:
+    checkTemplateLocation: false
+
 management:
   endpoints:
     web:

clinical-domain-agent/src/test/java/care/smith/fts/cda/impl/DeidentifhirStepFactoryTest.java

@@ -6,27 +6,26 @@
 import care.smith.fts.api.cda.Deidentificator;
 import care.smith.fts.cda.impl.DeidentifhirStepConfig.TCAConfig;
 import care.smith.fts.util.HttpClientConfig;
+import care.smith.fts.util.HttpClientFactory;
 import care.smith.fts.util.tca.TCADomains;
 import io.micrometer.core.instrument.MeterRegistry;
 import java.io.File;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.web.reactive.function.client.WebClientSsl;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.web.reactive.function.client.WebClient;
 
 @SpringBootTest
 class DeidentifhirStepFactoryTest {
 
   @Autowired private MeterRegistry meterRegistry;
-  @Autowired private WebClientSsl ssl;
+  @Autowired private HttpClientFactory clientProvider;
 
   private DeidentifhirStepFactory factory;
 
   @BeforeEach
   void setUp() {
-    factory = new DeidentifhirStepFactory(WebClient.builder(), ssl, meterRegistry);
+    factory = new DeidentifhirStepFactory(clientProvider, meterRegistry);
   }
 
   @Test

clinical-domain-agent/src/test/java/care/smith/fts/cda/impl/DeidentifhirStepTest.java

@@ -1,5 +1,6 @@
 package care.smith.fts.cda.impl;
 
+import static care.smith.fts.test.MockServerUtil.clientConfig;
 import static care.smith.fts.test.TestPatientGenerator.generateOnePatient;
 import static com.typesafe.config.ConfigFactory.parseResources;
 import static java.time.Duration.ofDays;
@@ -11,8 +12,9 @@
 
 import care.smith.fts.api.ConsentedPatient;
 import care.smith.fts.api.ConsentedPatientBundle;
+import care.smith.fts.cda.ClinicalDomainAgent;
 import care.smith.fts.cda.services.deidentifhir.DeidentifhirUtils;
-import care.smith.fts.test.MockServerUtil;
+import care.smith.fts.util.HttpClientFactory;
 import care.smith.fts.util.tca.TCADomains;
 import io.micrometer.core.instrument.MeterRegistry;
 import java.io.IOException;
@@ -25,22 +27,20 @@
 import org.mockserver.junit.jupiter.MockServerExtension;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.web.reactive.function.client.WebClient;
 
-@SpringBootTest
+@SpringBootTest(classes = ClinicalDomainAgent.class)
 @ExtendWith(MockServerExtension.class)
 class DeidentifhirStepTest {
 
   @Autowired MeterRegistry meterRegistry;
   private DeidentifhirStep step;
 
   @BeforeEach
-  void setUp(MockServerClient mockServer) {
+  void setUp(MockServerClient mockServer, @Autowired HttpClientFactory clientProvider) {
     var scraperConfig = parseResources(DeidentifhirUtils.class, "IDScraper.profile");
     var deidentifhirConfig = parseResources(DeidentifhirUtils.class, "CDtoTransport.profile");
-    var server = MockServerUtil.clientConfig(mockServer);
     var domains = new TCADomains("domain", "domain", "domain");
-    var client = server.createClient(WebClient.builder(), null);
+    var client = clientProvider.createClient(clientConfig(mockServer));
     step =
         new DeidentifhirStep(
             client, domains, ofDays(14), deidentifhirConfig, scraperConfig, meterRegistry);
@@ -100,7 +100,7 @@ void deidentifySucceeds(MockServerClient mockServer) throws IOException {
                     json(
                         """
                             {
-                              "resarchMappingName": "resarchMappingName",
+                              "transferId": "transferId",
                               "transportMapping": { "id1.identifier.identifierSystem:id1": "tident1",
                                                     "id1.Patient:id1": "tid1" },
                               "dateShiftValue": 1209600.000000000