Merge branch 'develop' into ps/test-cleanups

# Conflicts:
#	build.gradle

build.gradle

@@ -8,8 +8,8 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.51.0'
     id 'com.jfrog.artifactory' version '5.2.5'
     id 'org.sonarqube' version '5.1.0.4882'
-    id 'io.spring.dependency-management' version '1.1.6'
-    id 'org.springframework.boot' version '3.3.3'
+    id 'io.spring.dependency-management' version '1.1.7'
+    id 'org.springframework.boot' version '3.4.1'
     id 'com.srcclr.gradle' version '3.1.12'
 }
 
@@ -19,10 +19,6 @@ project.ext {
     isCiServer = System.getenv().containsKey("CI")
 }
 
-// Spring Boot 3.2.3 pulls in opentelemetry-bom 1.31.0.
-// We need >= 1.32.0 so that our HttpServerMetrics can use Meter.setExplicitBucketBoundariesAdvice:
-ext['opentelemetry.version'] = '1.41.0'
-
 // If true, search local repository (~/.m2/repository/) first for dependencies.
 def useMavenLocal = false
 repositories {
@@ -50,14 +46,15 @@ dependencies {
 
     // Spring
     implementation group: 'org.springframework.retry', name: 'spring-retry'
+    implementation group: 'org.springframework.boot', name: 'spring-boot-autoconfigure'
     implementation group: 'org.springframework.boot', name: 'spring-boot-starter-data-jdbc'
     implementation group: 'org.springframework.boot', name: 'spring-boot-starter-web'
     annotationProcessor group: 'org.springframework.boot', name: 'spring-boot-configuration-processor'
 
     // Misc. Services
-    implementation group: 'io.kubernetes', name: 'client-java', version: '20.0.1'
+    implementation group: 'io.kubernetes', name: 'client-java', version: '21.0.2'
     constraints {
-        implementation('org.bouncycastle:bcprov-jdk18on:1.78.1') {
+        implementation('org.bouncycastle:bcprov-jdk18on:1.79') {
             because 'https://broadworkbench.atlassian.net/browse/DCJ-275'
         }
     }
@@ -66,7 +63,7 @@ dependencies {
 
     // Google dependencies
     // use common bom
-    implementation platform('com.google.cloud:libraries-bom:26.45.0')
+    implementation platform('com.google.cloud:libraries-bom:26.52.0')
     implementation group: 'com.google.cloud', name: 'google-cloud-core'
     implementation group: 'com.google.cloud', name: 'google-cloud-pubsub'
     api group: 'com.google.guava', name: 'guava'
@@ -76,38 +73,37 @@ dependencies {
     runtimeOnly group: 'org.postgresql', name: 'postgresql'
 
     // Terra libraries
-    implementation group: 'org.broadinstitute.dsde.workbench', name: 'sam-client_2.13', version: '0.1-0c4b377'
-    var stairwayVersion= '1.1.12-SNAPSHOT'
+    implementation group: 'org.broadinstitute.dsde.workbench', name: 'sam-client_2.13', version: 'v0.0.329'
+    var stairwayVersion= '1.1.17-SNAPSHOT'
     api "bio.terra:stairway-gcp:${stairwayVersion}"
     implementation "bio.terra:stairway-azure:${stairwayVersion}"
 
     // Logging
-    implementation group: 'com.google.apis', name: 'google-api-services-logging', version: 'v2-rev20240503-2.0.0'
+    implementation group: 'com.google.apis', name: 'google-api-services-logging', version: 'v2-rev20241018-2.0.0'
     implementation group: 'ch.qos.logback.contrib', name: 'logback-json-classic', version: '0.1.5'
     implementation group: 'ch.qos.logback.contrib', name: 'logback-jackson', version: '0.1.5'
 
-    // OpenTelemetry BOMs (opentelemetry-bom versioned by Spring dependency manager)
-    implementation platform('io.opentelemetry:opentelemetry-bom-alpha:1.41.0-alpha')
-    implementation platform('io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom:2.7.0')
-    implementation platform('io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom-alpha:2.7.0-alpha')
-    // OpenTelemetry dependencies versioned by BOMs
+    // OpenTelemetry dependencies:
+    // Spring Boot 3.4.0 pulls in opentelemetry-bom 1.43.0.
+    // We choose opentelemetry-instrumentation-bom-alpha:2.9.0-alpha because otel-instrumentation 2.9.0 targets otel 1.43.0.
+    // When upgrading Spring Boot, re-check these versions.
+    implementation platform("io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom-alpha:2.9.0-alpha")
+    // ... versioned by Spring Boot
     api 'io.opentelemetry:opentelemetry-api'
-    implementation 'io.opentelemetry:opentelemetry-sdk'
-    implementation 'io.opentelemetry:opentelemetry-sdk-metrics'
     implementation 'io.opentelemetry:opentelemetry-exporter-logging'
-    implementation 'io.opentelemetry.instrumentation:opentelemetry-spring-webmvc-6.0'
-    implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-api'
+    implementation 'io.opentelemetry:opentelemetry-exporter-otlp'
+    implementation 'io.opentelemetry:opentelemetry-sdk-extension-autoconfigure'
+    // ... versioned by opentelemetry-instrumentation-bom-alpha
     implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-annotations'
+    implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-api'
     implementation 'io.opentelemetry.instrumentation:opentelemetry-spring-boot-autoconfigure'
-    implementation 'io.opentelemetry:opentelemetry-exporter-prometheus'
+    implementation 'io.opentelemetry.semconv:opentelemetry-semconv'
     implementation 'io.opentelemetry:opentelemetry-api-incubator'
-    implementation 'io.opentelemetry:opentelemetry-sdk-extension-autoconfigure'
-    implementation 'io.opentelemetry:opentelemetry-exporter-otlp'
-    implementation 'org.springframework.boot:spring-boot-autoconfigure'
+    implementation 'io.opentelemetry:opentelemetry-exporter-prometheus'
 
     // Google cloud open telemetry exporters
-    implementation 'com.google.cloud.opentelemetry:exporter-trace:0.31.0'
-    implementation 'com.google.cloud.opentelemetry:exporter-metrics:0.31.0'
+    implementation 'com.google.cloud.opentelemetry:exporter-trace:0.33.0'
+    implementation 'com.google.cloud.opentelemetry:exporter-metrics:0.33.0'
 
     // Testing
     testImplementation 'org.springframework:spring-aspects' // for tracing in tests

settings.gradle

@@ -1,4 +1,4 @@
 rootProject.name = 'terra-common-lib'
 
 gradle.ext.projectGroup = 'bio.terra'
-gradle.ext.tclVersion = '1.1.19-SNAPSHOT'
+gradle.ext.tclVersion = '1.1.27-SNAPSHOT'

src/test/java/bio/terra/common/logging/HumanReadableLoggingTest.java

@@ -10,13 +10,13 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
-import org.springframework.boot.test.mock.mockito.SpyBean;
 import org.springframework.boot.test.system.CapturedOutput;
 import org.springframework.boot.test.system.OutputCaptureExtension;
 import org.springframework.boot.test.web.client.TestRestTemplate;
 import org.springframework.http.ResponseEntity;
 import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.bean.override.mockito.MockitoSpyBean;
 
 /**
  * A test to verify that the human-readable-logging Spring Profile will disable the configuration of
@@ -32,7 +32,7 @@ class HumanReadableLoggingTest {
 
   @Autowired private TestRestTemplate testRestTemplate;
   // Spy bean to allow us to mock out the RequestIdFilter ID generator.
-  @SpyBean private RequestIdFilter requestIdFilter;
+  @MockitoSpyBean private RequestIdFilter requestIdFilter;
 
   @BeforeEach
   void setUp() {

src/test/java/bio/terra/common/logging/LoggingTest.java

@@ -16,12 +16,12 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
-import org.springframework.boot.test.mock.mockito.SpyBean;
 import org.springframework.boot.test.system.CapturedOutput;
 import org.springframework.boot.test.system.OutputCaptureExtension;
 import org.springframework.boot.test.web.client.TestRestTemplate;
 import org.springframework.http.ResponseEntity;
 import org.springframework.test.context.ActiveProfiles;
+import org.springframework.test.context.bean.override.mockito.MockitoSpyBean;
 import org.springframework.test.context.junit.jupiter.SpringJUnitConfig;
 
 /**
@@ -52,7 +52,7 @@ class LoggingTest {
 
   @Autowired private TestRestTemplate testRestTemplate;
   // Spy bean to allow us to mock out the RequestIdFilter ID generator.
-  @SpyBean private RequestIdFilter requestIdFilter;
+  @MockitoSpyBean private RequestIdFilter requestIdFilter;
 
   @BeforeEach
   public void setUp() {