[CU-86b9ybg6d] Migrate to java-libraries-monorepo 4.0.0-rc2

pom.xml

@@ -5,9 +5,9 @@
   <modelVersion>4.0.0</modelVersion>
 
   <parent>
-    <groupId>org.springframework.boot</groupId>
-    <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.5.13</version>
+    <groupId>com.dnastack.starter</groupId>
+    <artifactId>spring-boot-parent</artifactId>
+    <version>4.0.0-rc2-9-gd79f5a8</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 
@@ -18,35 +18,11 @@
 
   <dependencyManagement>
     <dependencies>
-      <dependency>
-        <groupId>org.springframework.cloud</groupId>
-        <artifactId>spring-cloud-dependencies</artifactId>
-        <version>${spring-cloud.version}</version>
-        <type>pom</type>
-        <scope>import</scope>
-      </dependency>
       <dependency>
         <groupId>joda-time</groupId>
         <artifactId>joda-time</artifactId>
         <version>${version.joda}</version>
       </dependency>
-      <dependency>
-        <groupId>org.jdbi</groupId>
-        <artifactId>jdbi3-bom</artifactId>
-        <type>pom</type>
-        <version>${jdbi.version}</version>
-        <scope>import</scope>
-      </dependency>
-      <dependency>
-        <groupId>ch.qos.logback</groupId>
-        <artifactId>logback-classic</artifactId>
-        <version>${logback.version}</version>
-      </dependency>
-      <dependency>
-        <groupId>ch.qos.logback</groupId>
-        <artifactId>logback-core</artifactId>
-        <version>${logback.version}</version>
-      </dependency>
     </dependencies>
   </dependencyManagement>
 
@@ -57,16 +33,7 @@
     <maven-resources-plugin.version>3.2.0</maven-resources-plugin.version>
     <maven-surefire-plugin.version>3.0.0-M7</maven-surefire-plugin.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <!-- DNAstack Libs-->
-    <dnastack-token-validator.version>1.0.18</dnastack-token-validator.version>
-    <audit-event-logger.version>1.0.20</audit-event-logger.version>
-    <oauth-client-factory.version>1.0.5</oauth-client-factory.version>
-    <!-- Pin Jackson to 2.18.x: dnastack-oauth-client-factory-spring-starter 1.0.5 uses
-         removed-in-2.19 PropertyNamingStrategy.SNAKE_CASE API. Remove when bumping the lib. -->
-    <jackson-bom.version>2.18.6</jackson-bom.version>
     <!-- Other -->
-    <spring-cloud.version>2021.0.9</spring-cloud.version>
-    <jdbi.version>3.49.5</jdbi.version>
     <version.okhttp>4.12.0</version.okhttp>
     <version.trino>359</version.trino>
     <version.guava>32.1.3-jre</version.guava>
@@ -76,10 +43,7 @@
     <assertj.version>3.27.7</assertj.version>
     <feign.version>13.6</feign.version>
     <feign-form.version>3.8.0</feign-form.version>
-    <logback-extensions.version>1.0.1</logback-extensions.version>
-    <logback.version>1.5.25</logback.version>
     <lombok.version>1.18.42</lombok.version>
-    <resilience4j.version>2.3.0</resilience4j.version>
 
     <!-- Testing - Java 23 support. These overrides can be removed when we upgrade spring-boot-starter-parent to a version that supports Java 23. -->
     <mockito.version>5.20.0</mockito.version>
@@ -169,7 +133,7 @@
     </dependency>
     <dependency>
       <groupId>io.micrometer</groupId>
-      <artifactId>micrometer-tracing-bridge-brave</artifactId>
+      <artifactId>micrometer-tracing-bridge-otel</artifactId>
     </dependency>
     <dependency>
       <groupId>joda-time</groupId>
@@ -261,62 +225,44 @@
     <dependency>
       <groupId>io.github.resilience4j</groupId>
       <artifactId>resilience4j-retry</artifactId>
-      <version>${resilience4j.version}</version>
     </dependency>
     <dependency>
       <groupId>io.github.resilience4j</groupId>
       <artifactId>resilience4j-core</artifactId>
-      <version>${resilience4j.version}</version>
     </dependency>
 
     <!--Supporting-->
     <dependency>
       <groupId>com.dnastack</groupId>
       <artifactId>dnastack-token-validator</artifactId>
-      <version>${dnastack-token-validator.version}</version>
     </dependency>
 
     <!-- Audit Event Logger -->
     <dependency>
       <groupId>com.dnastack</groupId>
       <artifactId>spring-boot-audit-event-logger</artifactId>
-      <version>${audit-event-logger.version}</version>
-      <exclusions>
-        <exclusion>
-          <groupId>io.zipkin.reporter2</groupId>
-          <artifactId>zipkin-reporter-metrics-micrometer</artifactId>
-        </exclusion>
-        <exclusion>
-          <groupId>io.zipkin.reporter2</groupId>
-          <artifactId>zipkin-reporter</artifactId>
-        </exclusion>
-      </exclusions>
     </dependency>
 
     <dependency>
       <groupId>com.dnastack</groupId>
       <artifactId>dnastack-oauth-client-factory-spring-starter</artifactId>
-      <version>${oauth-client-factory.version}</version>
     </dependency>
 
     <!-- Customized Logging -->
     <dependency>
       <groupId>com.dnastack</groupId>
       <artifactId>logback-extensions</artifactId>
-      <version>${logback-extensions.version}</version>
     </dependency>
 
     <!-- Zonky Test-->
     <dependency>
       <groupId>io.zonky.test</groupId>
       <artifactId>embedded-database-spring-test</artifactId>
-      <version>2.6.0</version>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>io.zonky.test</groupId>
       <artifactId>embedded-postgres</artifactId>
-      <version>2.1.1</version>
       <scope>test</scope>
     </dependency>
 

src/main/java/com/dnastack/ga4gh/dataconnect/ApplicationConfig.java

@@ -1,10 +1,10 @@
 package com.dnastack.ga4gh.dataconnect;
 
-import brave.Tracing;
 import com.dnastack.auth.JwtTokenParser;
 import com.dnastack.auth.JwtTokenParserFactory;
 import com.dnastack.auth.PermissionChecker;
 import com.dnastack.auth.PermissionCheckerFactory;
+import com.dnastack.auth.client.OidcHttpClient;
 import com.dnastack.auth.client.TokenActionsHttpClientFactory;
 import com.dnastack.auth.keyresolver.CachingIssuerPubKeyJwksResolver;
 import com.dnastack.auth.keyresolver.IssuerPubKeyStaticResolver;
@@ -21,8 +21,10 @@
 import io.jsonwebtoken.JwsHeader;
 import io.jsonwebtoken.JwtException;
 import io.micrometer.core.instrument.MeterRegistry;
+import io.micrometer.observation.ObservationRegistry;
 import lombok.Getter;
 import lombok.extern.slf4j.Slf4j;
+import okhttp3.ConnectionPool;
 import okhttp3.OkHttpClient;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
@@ -96,9 +98,14 @@ public OkHttpClient httpClient() {
     }
 
     @Bean
-    public TrinoClient getTrinoClient(OkHttpClient httpClient, Tracing tracing, ServiceAccountAuthenticator accountAuthenticator, MeterRegistry registry) {
+    public TrinoClient getTrinoClient(OkHttpClient httpClient, io.micrometer.tracing.Tracer tracer, ServiceAccountAuthenticator accountAuthenticator, MeterRegistry registry) {
         return new TrinoTelemetryClient(
-            new TrinoHttpClient(tracing, httpClient, trinoDatasourceUrl, accountAuthenticator), registry);
+            new TrinoHttpClient(tracer, httpClient, trinoDatasourceUrl, accountAuthenticator), registry);
+    }
+
+    @Bean
+    public ConnectionPool tokenValidatorConnectionPool() {
+        return new ConnectionPool();
     }
 
     @Bean
@@ -210,7 +217,12 @@ public SecurityFilterChain configure(HttpSecurity http) throws Exception {
         }
 
         @Bean
-        public List<IssuerInfo> allowedIssuers(AuthConfig authConfig) {
+        public OidcHttpClient oidcHttpClient(ObservationRegistry observationRegistry, ConnectionPool tokenValidatorConnectionPool) {
+            return new OidcHttpClient(observationRegistry, tokenValidatorConnectionPool);
+        }
+
+        @Bean
+        public List<IssuerInfo> allowedIssuers(AuthConfig authConfig, OidcHttpClient oidcHttpClient) {
             List<AuthConfig.IssuerConfig> issuers = authConfig.getTokenIssuers();
             if (issuers == null || issuers.isEmpty()) {
                 throw new IllegalArgumentException("At least one token issuer must be defined");
@@ -224,7 +236,7 @@ public List<IssuerInfo> allowedIssuers(AuthConfig authConfig) {
                         .allowedAudiences(issuerConfig.getAudiences())
                         .publicKeyResolver(issuerConfig.getRsaPublicKey() != null
                             ? new IssuerPubKeyStaticResolver(issuerUri, issuerConfig.getRsaPublicKey())
-                            : new CachingIssuerPubKeyJwksResolver(issuerUri))
+                            : CachingIssuerPubKeyJwksResolver.create(issuerUri, oidcHttpClient))
                         .build();
                 })
                 .toList();
@@ -236,10 +248,11 @@ public PermissionChecker permissionChecker(
             List<IssuerInfo> allowedIssuers,
             @Value("${app.url}") String policyEvaluationRequester,
             @Value("${app.auth.token-issuers[0].issuer-uri}") String walletUrl,
-            Tracing tracing
+            ObservationRegistry observationRegistry,
+            ConnectionPool tokenValidatorConnectionPool
         ) {
             String policyEvaluationUrl = stripTrailingSlashes(walletUrl) + "/policies/evaluations";
-            return PermissionCheckerFactory.create(allowedIssuers, policyEvaluationRequester, policyEvaluationUrl, tracing);
+            return PermissionCheckerFactory.create(allowedIssuers, policyEvaluationRequester, policyEvaluationUrl, observationRegistry, tokenValidatorConnectionPool);
         }
 
         private String stripTrailingSlashes(String url) {
@@ -251,8 +264,9 @@ private String stripTrailingSlashes(String url) {
         }
 
         @Bean
-        public JwtDecoder jwtDecoder(List<IssuerInfo> allowedIssuers, PermissionChecker permissionChecker, Tracing tracing) {
-            final JwtTokenParser jwtTokenParser = JwtTokenParserFactory.create(allowedIssuers, TokenActionsHttpClientFactory.create(tracing));
+        public JwtDecoder jwtDecoder(List<IssuerInfo> allowedIssuers, PermissionChecker permissionChecker, ObservationRegistry observationRegistry, ConnectionPool tokenValidatorConnectionPool) {
+            final JwtTokenParser jwtTokenParser = JwtTokenParserFactory.create(allowedIssuers,
+                TokenActionsHttpClientFactory.create(observationRegistry, tokenValidatorConnectionPool));
             return (jwtToken) -> {
                 try {
                     permissionChecker.checkPermissions(jwtToken);

src/main/java/com/dnastack/ga4gh/dataconnect/adapter/shared/DataConnectAuthRequest.java

@@ -1,13 +1,13 @@
 package com.dnastack.ga4gh.dataconnect.adapter.shared;
 
-import com.fasterxml.jackson.databind.PropertyNamingStrategy;
+import com.fasterxml.jackson.databind.PropertyNamingStrategies;
 import com.fasterxml.jackson.databind.annotation.JsonNaming;
 import lombok.Value;
 
 import java.util.Map;
 
 @Value
-@JsonNaming(PropertyNamingStrategy.KebabCaseStrategy.class)
+@JsonNaming(PropertyNamingStrategies.KebabCaseStrategy.class)
 public class DataConnectAuthRequest {
     String key;
     String resourceType;

src/main/java/com/dnastack/ga4gh/dataconnect/adapter/shared/GlobalControllerExceptionHandler.java

@@ -1,6 +1,6 @@
 package com.dnastack.ga4gh.dataconnect.adapter.shared;
 
-import brave.Tracer;
+import io.micrometer.tracing.Tracer;
 import com.dnastack.ga4gh.dataconnect.adapter.trino.exception.TableApiErrorException;
 import com.dnastack.ga4gh.dataconnect.model.TableError;
 import lombok.extern.slf4j.Slf4j;
@@ -24,12 +24,12 @@ public ResponseEntity<?> handleAuthRequiredException(AuthRequiredException e) {
         return ResponseEntity.status(401)
             .contentType(MediaType.APPLICATION_JSON_UTF8)
             .header("WWW-Authenticate", "GA4GH-Search realm=\"" + escapeQuotes(cr.getKey()) + "\"")
-            .body(Map.of("authorization-request", cr, "trace_id", tracer.currentSpan().context().traceIdString()));
+            .body(Map.of("authorization-request", cr, "trace_id", tracer.currentSpan().context().traceId()));
     }
 
     @ExceptionHandler({TableApiErrorException.class})
     public ResponseEntity<?> handleTableApiErrorException(TableApiErrorException throwable) {
-        String traceId = tracer.currentSpan().context().traceIdString();
+        String traceId = tracer.currentSpan().context().traceId();
         TableError error = TableError.fromThrowable(throwable.getCause(), null);
         log.error("Generating response with error that escaped controller: {}", error, throwable);
 

src/main/java/com/dnastack/ga4gh/dataconnect/adapter/trino/TrinoDataConnectAdapter.java

@@ -1,6 +1,5 @@
 package com.dnastack.ga4gh.dataconnect.adapter.trino;
 
-import brave.Tracing;
 import com.dnastack.auth.cache.CachingConcurrentHashMap;
 import com.dnastack.ga4gh.dataconnect.ApplicationConfig;
 import com.dnastack.ga4gh.dataconnect.DataModelSupplier;
@@ -15,6 +14,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.JsonNodeType;
 import com.google.common.collect.Streams;
+import io.micrometer.tracing.Tracer;
 import jakarta.servlet.http.HttpServletRequest;
 import lombok.Getter;
 import lombok.SneakyThrows;
@@ -86,14 +86,14 @@ public String toString() {
 
     private final ObjectMapper objectMapper;
 
-    private final Tracing tracer;
+    private final Tracer tracer;
 
     public TrinoDataConnectAdapter(
         TrinoClient client,
         Jdbi jdbi,
         ApplicationConfig applicationConfig,
         List<DataModelSupplier> dataModelSuppliers,
-        Tracing tracer,
+        Tracer tracer,
         // We use CachingConcurrentHashMap to cache the schema and catalog names to increase performance
         // When paginating through the tables
         @Value("${app.caching.expire-after:PT5M}") Duration expireAfter,
@@ -309,7 +309,7 @@ private QueryJob createQueryJob(String queryId, String query, DataModel dataMode
         QueryJob queryJob = QueryJob.builder()
             .query(query)
             .id(queryId)
-            .originalTraceId(tracer.currentTraceContext().get().traceIdString())
+            .originalTraceId(tracer.currentTraceContext().context().traceId())
             .startedAt(currentTime)
             .lastActivityAt(currentTime)
             .schema(tableSchema)