70 remove jaeger due to deprecation

build.gradle

@@ -1,6 +1,6 @@
 plugins {
-    id "org.springframework.boot" version "2.7.13"
-    id "io.spring.dependency-management" version "1.1.0"
+    id "org.springframework.boot" version "3.1.3"
+    id "io.spring.dependency-management" version "1.1.3"
     id "java"
     id "jacoco"
     id "com.diffplug.spotless" version "6.19.0"
@@ -18,7 +18,7 @@ configurations {
 }
 
 ext {
-    set("springCloudVersion", "2021.0.7")
+    set("springCloudVersion", "2022.0.3")
     set("hapiVersion", "6.6.1")
 }
 
@@ -49,15 +49,9 @@ dependencies {
     implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r4:${hapiVersion}"
     implementation "ca.uhn.hapi.fhir:hapi-fhir-client-okhttp:${hapiVersion}"
 
-    implementation "io.opentracing.contrib:opentracing-spring-web-starter:4.1.0"
-    implementation "io.opentracing.contrib:opentracing-spring-jaeger-web-starter:3.3.1"
-    implementation "io.opentracing.contrib:opentracing-spring-jaeger-cloud-starter:3.3.1"
-    implementation "io.opentracing.contrib:opentracing-okhttp3:3.0.0"
-    implementation "io.jaegertracing:jaeger-client:1.8.1"
-
     developmentOnly "org.springframework.boot:spring-boot-devtools"
     runtimeOnly "org.postgresql:postgresql:42.6.0"
-    runtimeOnly "com.h2database:h2:2.1.214"
+    runtimeOnly 'com.h2database:h2:2.2.222'
     annotationProcessor "org.springframework.boot:spring-boot-configuration-processor"
     testImplementation "org.springframework.boot:spring-boot-starter-test"
 }

deploy/docker-compose.exposed.yml

@@ -1,9 +1,4 @@
 services:
-  jaeger:
-    ports:
-      - 127.0.0.1:16686:16686
-      - 127.0.0.1:6831:6831/udp
-
   fhir-db:
     ports:
       - 127.0.0.1:15432:5432

deploy/docker-compose.gw-deps.yml

@@ -1,28 +1,17 @@
 services:
-  jaeger:
-    image: jaegertracing/all-in-one:1.45@sha256:5d5c9d2d8c8cbb42f1db4aac1f1f8487bac63da6802004d0da8580fc0c7311a1
-
   fhir-pseudonymizer:
     image: ghcr.io/miracum/fhir-pseudonymizer:v2.17.0@sha256:431a7f4516c1f641966c507941b87a997441665656572a1c00c44376ef08fe24
     environment:
-      Tracing__IsEnabled: "true"
-      Tracing__Jaeger__AgentHost: jaeger
-      Tracing__Jaeger__AgentPort: 6831
       Vfps__Address: "dns:///vfps:8081"
       UseSystemTextJsonFhirSerializer: "true"
       PseudonymizationService: "Vfps"
     volumes:
       - ${PWD}/deploy/anonymization.yaml:/etc/anonymization.yaml:ro
     depends_on:
-      - jaeger
       - vfps
 
   loinc-converter:
     image: harbor.miracum.org/miracum-etl/loinc-conversion:v1.14.2@sha256:9815eb71c13fa2a0b74df6492f41cc2d7b9969696984e6045b6217600ad1f0e1
-    environment:
-      JAEGER_AGENT_HOST: jaeger
-    depends_on:
-      - jaeger
 
   vfps-db:
     image: docker.io/library/postgres:15.3@sha256:31c9342603866f29206a06b77c8fed48b3c3f70d710a4be4e8216b134f92d0df
@@ -67,8 +56,6 @@ services:
       ConnectionStrings__PostgreSQL: "Host=vfps-db:5432;Database=vfps;Timeout=60;Max Auto Prepare=5;Application Name=vfps;Maximum Pool Size=50;"
       PGUSER: postgres
       PGPASSWORD: postgres
-      Tracing__IsEnabled: "true"
-      Tracing__Jaeger__AgentHost: "jaeger"
       Pseudonymization__Caching__Namespaces__IsEnabled: "true"
     depends_on:
       - vfps-db

deploy/docker-compose.yml

@@ -14,10 +14,7 @@ services:
       SERVICES_PSQL_ENABLED: ${SERVICES_PSQL_ENABLED:-true}
       SERVICES_KAFKA_ENABLED: ${SERVICES_KAFKA_ENABLED:-false}
       BOOTSTRAP_SERVERS: ${BOOTSTRAP_SERVERS:-kafka1:19092}
-      OPENTRACING_JAEGER_ENABLED: ${OPENTRACING_JAEGER_ENABLED:-true}
-      OPENTRACING_JAEGER_UDP_SENDER_HOST: ${OPENTRACING_JAEGER_UDP_SENDER_HOST:-jaeger}
     depends_on:
       - loinc-converter
       - fhir-db
-      - jaeger
       - fhir-pseudonymizer

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
 networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -85,9 +85,6 @@ done
 APP_BASE_NAME=${0##*/}
 APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
 
@@ -133,26 +130,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -197,6 +197,10 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
 # Collect all arguments for the java command;
 #   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
 #     shell script including quotes and variable substitutions, so put them in

src/main/java/org/miracum/etl/fhirgateway/AppConfig.java

@@ -8,31 +8,19 @@
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
-import io.jaegertracing.internal.propagation.TraceContextCodec;
 import io.micrometer.core.instrument.Metrics;
 import io.micrometer.core.instrument.binder.okhttp3.OkHttpMetricsEventListener;
-import io.opentracing.Span;
-import io.opentracing.contrib.java.spring.jaeger.starter.TracerBuilderCustomizer;
-import io.opentracing.contrib.okhttp3.OkHttpClientSpanDecorator;
-import io.opentracing.contrib.okhttp3.TracingInterceptor;
-import io.opentracing.propagation.Format;
-import io.opentracing.util.GlobalTracer;
-import java.util.Arrays;
 import java.util.HashMap;
 import java.util.concurrent.TimeUnit;
-import okhttp3.Connection;
 import okhttp3.ConnectionPool;
 import okhttp3.OkHttpClient;
-import okhttp3.Request;
-import okhttp3.Response;
 import org.miracum.etl.fhirgateway.processors.FhirPseudonymizer;
 import org.miracum.etl.fhirgateway.processors.IPseudonymizer;
 import org.miracum.etl.fhirgateway.processors.NoopPseudonymizer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
 import org.springframework.boot.web.client.RestTemplateBuilder;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -60,37 +48,15 @@ public FhirContext fhirContext(
           boolean useLoadBalancerConnectionPool) {
     var fhirContext = FhirContext.forR4();
 
-    var opNameDecorator =
-        new OkHttpClientSpanDecorator() {
-          @Override
-          public void onRequest(Request request, Span span) {
-            // add the operation name to the span
-            span.setOperationName(request.url().encodedPath());
-          }
-
-          @Override
-          public void onError(Throwable throwable, Span span) {}
-
-          @Override
-          public void onResponse(Connection connection, Response response, Span span) {}
-        };
-
     var connectionPool = new ConnectionPool();
     if (useLoadBalancerConnectionPool) {
       connectionPool =
           new ConnectionPool(
               MAX_IDLE_CONNECTIONS, KEEP_ALIVE_DURATION_MILLISECONDS, TimeUnit.MILLISECONDS);
     }
 
-    var tracingInterceptor =
-        new TracingInterceptor(
-            GlobalTracer.get(),
-            Arrays.asList(OkHttpClientSpanDecorator.STANDARD_TAGS, opNameDecorator));
-
     var okclient =
         new OkHttpClient.Builder()
-            .addInterceptor(tracingInterceptor)
-            .addNetworkInterceptor(tracingInterceptor)
             .connectionPool(connectionPool)
             .eventListener(
                 OkHttpMetricsEventListener.builder(Metrics.globalRegistry, "fhir.client").build())
@@ -103,21 +69,6 @@ public void onResponse(Connection connection, Response response, Span span) {}
     return fhirContext;
   }
 
-  @Bean
-  public TracerBuilderCustomizer traceContextJaegerTracerCustomizer() {
-    return builder -> {
-      var injector = new TraceContextCodec.Builder().build();
-
-      builder
-          .registerInjector(Format.Builtin.HTTP_HEADERS, injector)
-          .registerExtractor(Format.Builtin.HTTP_HEADERS, injector);
-
-      builder
-          .registerInjector(Format.Builtin.TEXT_MAP, injector)
-          .registerExtractor(Format.Builtin.TEXT_MAP, injector);
-    };
-  }
-
   @Bean
   public RestTemplate restTemplate(RestTemplateBuilder builder) {
     return builder.build();
@@ -205,13 +156,4 @@ public IPseudonymizer fhirPseudonymizer(
       return new NoopPseudonymizer();
     }
   }
-
-  @Bean
-  @ConditionalOnProperty(
-      value = "opentracing.jaeger.enabled",
-      havingValue = "false",
-      matchIfMissing = false)
-  public io.opentracing.Tracer jaegerTracer() {
-    return io.opentracing.noop.NoopTracerFactory.create();
-  }
 }

src/main/java/org/miracum/etl/fhirgateway/processors/BaseKafkaProcessor.java

@@ -32,7 +32,7 @@ public Bundle process(Message<Resource> message) {
     }
 
     var incomingTopic = message.getHeaders().get(KafkaHeaders.RECEIVED_TOPIC);
-    var key = message.getHeaders().getOrDefault(KafkaHeaders.RECEIVED_MESSAGE_KEY, null);
+    var key = message.getHeaders().getOrDefault(KafkaHeaders.RECEIVED_KEY, null);
     var resource = message.getPayload();
 
     LOG.debug(

src/main/java/org/miracum/etl/fhirgateway/processors/KafkaProcessor.java

@@ -2,6 +2,7 @@
 
 import static net.logstash.logback.argument.StructuredArguments.kv;
 
+import java.util.Objects;
 import java.util.Optional;
 import java.util.function.Function;
 import org.apache.commons.lang3.StringUtils;
@@ -20,8 +21,8 @@
     "${services.kafka.enabled:true} and !T(org.springframework.util.StringUtils).isEmpty('${spring.cloud.stream.bindings.process-out-0.destination:}')")
 public class KafkaProcessor extends BaseKafkaProcessor {
 
-  private String generateTopicMatchExpression;
-  private String generateTopicReplacement;
+  private final String generateTopicMatchExpression;
+  private final String generateTopicReplacement;
 
   public KafkaProcessor(
       ResourcePipeline pipeline,
@@ -39,14 +40,13 @@ Function<Message<Resource>, Message<Bundle>> process() {
     return message -> {
       var processed = super.process(message);
 
-      var messageKey =
-          message.getHeaders().getOrDefault(KafkaHeaders.RECEIVED_MESSAGE_KEY, "").toString();
+      var messageKey = message.getHeaders().getOrDefault(KafkaHeaders.RECEIVED_KEY, "").toString();
 
       var messageBuilder =
-          MessageBuilder.withPayload(processed)
-              .setHeaderIfAbsent(KafkaHeaders.MESSAGE_KEY, messageKey);
+          MessageBuilder.withPayload(processed).setHeaderIfAbsent(KafkaHeaders.KEY, messageKey);
 
-      var inputTopic = message.getHeaders().get(KafkaHeaders.RECEIVED_TOPIC).toString();
+      var inputTopic =
+          Objects.requireNonNull(message.getHeaders().get(KafkaHeaders.RECEIVED_TOPIC)).toString();
 
       var outputTopic = computeOutputTopicFromInputTopic(inputTopic);
       // see https://github.com/spring-cloud/spring-cloud-stream/issues/1909 for

src/main/java/org/miracum/etl/fhirgateway/stores/FhirServerResourceRepository.java

@@ -54,6 +54,7 @@ public <T, E extends Throwable> void onError(
                 "Trying to sent resource to FHIR server caused error. {} attempt.",
                 context.getRetryCount(),
                 throwable);
+            assert saveFailedCounter != null;
             saveFailedCounter.incrementAndGet();
           }
         });

src/main/resources/application-dev.yml

@@ -23,12 +23,6 @@ services:
       match-expression: "fhir\\."
       replace-with: "fhir.post-gateway-pseuded-"
 
-opentracing:
-  jaeger:
-    probabilistic-sampler:
-      sampling-rate: 1
-    log-spans: true
-
 spring:
   datasource:
     url: jdbc:postgresql://localhost:15432/fhir

src/main/resources/application.yml

@@ -44,8 +44,8 @@ spring:
       key-serializer: org.apache.kafka.common.serialization.StringSerializer
       value-serializer: org.miracum.kafka.serializers.KafkaFhirSerializer
   cloud:
+    function.definition: process
     stream:
-      function.definition: process
       bindings:
         process-in-0:
           consumer:
@@ -102,12 +102,6 @@ fhir:
   systems:
     loinc: "http://loinc.org"
 
-opentracing:
-  jaeger:
-    udp-sender:
-      host: localhost
-    log-spans: false
-
 app:
   version: 0.0.0-dev