[PF-2983]: Bump the minor-patch-dependencies group across 1 directory…

… with 9 updates (#198)

* [PF-2983]: Bump the minor-patch-dependencies group across 1 directory with 9 updates

Bumps the minor-patch-dependencies group with 8 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [com.google.cloud:libraries-bom](https://github.com/googleapis/java-cloud-bom) | `26.44.0` | `26.45.0` |
| bio.terra:stairway-gcp | `1.1.10-SNAPSHOT` | `1.1.12-SNAPSHOT` |
| bio.terra:stairway-azure | `1.1.10-SNAPSHOT` | `1.1.12-SNAPSHOT` |
| [io.opentelemetry:opentelemetry-bom-alpha](https://github.com/open-telemetry/opentelemetry-java) | `1.37.0-alpha` | `1.41.0-alpha` |
| [io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom](https://github.com/open-telemetry/opentelemetry-java-instrumentation) | `2.3.0` | `2.7.0` |
| com.jfrog.artifactory | `5.2.3` | `5.2.5` |
| [io.spring.dependency-management](https://github.com/spring-gradle-plugins/dependency-management-plugin) | `1.1.5` | `1.1.6` |
| [org.springframework.boot](https://github.com/spring-projects/spring-boot) | `3.3.1` | `3.3.3` |



Updates `com.google.cloud:libraries-bom` from 26.44.0 to 26.45.0
- [Release notes](https://github.com/googleapis/java-cloud-bom/releases)
- [Changelog](https://github.com/googleapis/java-cloud-bom/blob/main/release-please-config.json)
- [Commits](googleapis/java-cloud-bom@v26.44.0...v26.45.0)

Updates `bio.terra:stairway-gcp` from 1.1.10-SNAPSHOT to 1.1.12-SNAPSHOT

Updates `bio.terra:stairway-azure` from 1.1.10-SNAPSHOT to 1.1.12-SNAPSHOT

Updates `bio.terra:stairway-azure` from 1.1.10-SNAPSHOT to 1.1.12-SNAPSHOT

Updates `io.opentelemetry:opentelemetry-bom-alpha` from 1.37.0-alpha to 1.41.0-alpha
- [Release notes](https://github.com/open-telemetry/opentelemetry-java/releases)
- [Changelog](https://github.com/open-telemetry/opentelemetry-java/blob/main/CHANGELOG.md)
- [Commits](https://github.com/open-telemetry/opentelemetry-java/commits)

Updates `io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom` from 2.3.0 to 2.7.0
- [Release notes](https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases)
- [Changelog](https://github.com/open-telemetry/opentelemetry-java-instrumentation/blob/main/CHANGELOG.md)
- [Commits](open-telemetry/opentelemetry-java-instrumentation@v2.3.0...v2.7.0)

Updates `io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom-alpha` from 2.3.0-alpha to 2.7.0-alpha
- [Release notes](https://github.com/open-telemetry/opentelemetry-java-instrumentation/releases)
- [Changelog](https://github.com/open-telemetry/opentelemetry-java-instrumentation/blob/main/CHANGELOG.md)
- [Commits](https://github.com/open-telemetry/opentelemetry-java-instrumentation/commits)

Updates `com.jfrog.artifactory` from 5.2.3 to 5.2.5

Updates `io.spring.dependency-management` from 1.1.5 to 1.1.6
- [Release notes](https://github.com/spring-gradle-plugins/dependency-management-plugin/releases)
- [Commits](spring-gradle-plugins/dependency-management-plugin@v1.1.5...v1.1.6)

Updates `org.springframework.boot` from 3.3.1 to 3.3.3
- [Release notes](https://github.com/spring-projects/spring-boot/releases)
- [Commits](spring-projects/spring-boot@v3.3.1...v3.3.3)

---
updated-dependencies:
- dependency-name: com.google.cloud:libraries-bom
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor-patch-dependencies
- dependency-name: bio.terra:stairway-gcp
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-patch-dependencies
- dependency-name: bio.terra:stairway-azure
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-patch-dependencies
- dependency-name: bio.terra:stairway-azure
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-patch-dependencies
- dependency-name: io.opentelemetry:opentelemetry-bom-alpha
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor-patch-dependencies
- dependency-name: io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor-patch-dependencies
- dependency-name: io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom-alpha
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor-patch-dependencies
- dependency-name: com.jfrog.artifactory
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-patch-dependencies
- dependency-name: io.spring.dependency-management
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-patch-dependencies
- dependency-name: org.springframework.boot
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-patch-dependencies
...

Signed-off-by: dependabot[bot] <[email protected]>

* Update build.gradle

update ext version to match current otel version

* Remove deprecated otel annotation; fix other otel deprecation warnings

* fix spring boot dependency

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Phil Shapiro <[email protected]>

build.gradle

@@ -6,10 +6,10 @@ plugins {
 
     id 'com.diffplug.spotless' version '6.25.0'
     id 'com.github.ben-manes.versions' version '0.51.0'
-    id 'com.jfrog.artifactory' version '5.2.3'
+    id 'com.jfrog.artifactory' version '5.2.5'
     id 'org.sonarqube' version '5.1.0.4882'
-    id 'io.spring.dependency-management' version '1.1.5'
-    id 'org.springframework.boot' version '3.3.1'
+    id 'io.spring.dependency-management' version '1.1.6'
+    id 'org.springframework.boot' version '3.3.3'
     id 'ru.vyarus.quality' version '5.0.0'
     id 'com.srcclr.gradle' version '3.1.12'
 }
@@ -22,7 +22,7 @@ project.ext {
 
 // 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'] = '1.37.0'
+ext['opentelemetry.version'] = '1.41.0'
 
 // If true, search local repository (~/.m2/repository/) first for dependencies.
 def useMavenLocal = false
@@ -67,7 +67,7 @@ dependencies {
 
     // Google dependencies
     // use common bom
-    implementation platform('com.google.cloud:libraries-bom:26.44.0')
+    implementation platform('com.google.cloud:libraries-bom:26.45.0')
     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'
@@ -78,7 +78,7 @@ dependencies {
 
     // Terra libraries
     implementation group: 'org.broadinstitute.dsde.workbench', name: 'sam-client_2.13', version: '0.1-0c4b377'
-    var stairwayVersion= '1.1.10-SNAPSHOT'
+    var stairwayVersion= '1.1.12-SNAPSHOT'
     api "bio.terra:stairway-gcp:${stairwayVersion}"
     implementation "bio.terra:stairway-azure:${stairwayVersion}"
 
@@ -88,9 +88,9 @@ dependencies {
     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:1.37.0-alpha')
-    implementation platform('io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom:2.3.0')
-    implementation platform('io.opentelemetry.instrumentation:opentelemetry-instrumentation-bom-alpha:2.3.0-alpha')
+    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
     api 'io.opentelemetry:opentelemetry-api'
     implementation 'io.opentelemetry:opentelemetry-sdk'
@@ -99,7 +99,7 @@ dependencies {
     implementation 'io.opentelemetry.instrumentation:opentelemetry-spring-webmvc-6.0'
     implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-api'
     implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-annotations'
-    implementation 'io.opentelemetry.instrumentation:opentelemetry-spring-boot'
+    implementation 'io.opentelemetry.instrumentation:opentelemetry-spring-boot-autoconfigure'
     implementation 'io.opentelemetry:opentelemetry-exporter-prometheus'
     implementation 'io.opentelemetry:opentelemetry-api-incubator'
     implementation 'io.opentelemetry:opentelemetry-sdk-extension-autoconfigure'

src/main/java/bio/terra/common/opentelemetry/HttpMetricsAdvice.java

@@ -10,7 +10,10 @@
 
 import io.opentelemetry.api.incubator.metrics.ExtendedDoubleHistogramBuilder;
 import io.opentelemetry.api.metrics.DoubleHistogramBuilder;
-import io.opentelemetry.semconv.SemanticAttributes;
+import io.opentelemetry.semconv.HttpAttributes;
+import io.opentelemetry.semconv.NetworkAttributes;
+import io.opentelemetry.semconv.ServerAttributes;
+import io.opentelemetry.semconv.UrlAttributes;
 import java.util.List;
 import java.util.stream.DoubleStream;
 
@@ -52,13 +55,13 @@ static void applyClientDurationAdvice(DoubleHistogramBuilder builder) {
     ((ExtendedDoubleHistogramBuilder) builder)
         .setAttributesAdvice(
             asList(
-                SemanticAttributes.HTTP_REQUEST_METHOD,
-                SemanticAttributes.HTTP_RESPONSE_STATUS_CODE,
+                HttpAttributes.HTTP_REQUEST_METHOD,
+                HttpAttributes.HTTP_RESPONSE_STATUS_CODE,
                 ERROR_TYPE,
-                SemanticAttributes.NETWORK_PROTOCOL_NAME,
-                SemanticAttributes.NETWORK_PROTOCOL_VERSION,
-                SemanticAttributes.SERVER_ADDRESS,
-                SemanticAttributes.SERVER_PORT));
+                NetworkAttributes.NETWORK_PROTOCOL_NAME,
+                NetworkAttributes.NETWORK_PROTOCOL_VERSION,
+                ServerAttributes.SERVER_ADDRESS,
+                ServerAttributes.SERVER_PORT));
   }
 
   static void applyServerDurationAdvice(DoubleHistogramBuilder builder) {
@@ -68,13 +71,13 @@ static void applyServerDurationAdvice(DoubleHistogramBuilder builder) {
     ((ExtendedDoubleHistogramBuilder) builder)
         .setAttributesAdvice(
             asList(
-                SemanticAttributes.HTTP_ROUTE,
-                SemanticAttributes.HTTP_REQUEST_METHOD,
-                SemanticAttributes.HTTP_RESPONSE_STATUS_CODE,
+                HttpAttributes.HTTP_ROUTE,
+                HttpAttributes.HTTP_REQUEST_METHOD,
+                HttpAttributes.HTTP_RESPONSE_STATUS_CODE,
                 ERROR_TYPE,
-                SemanticAttributes.NETWORK_PROTOCOL_NAME,
-                SemanticAttributes.NETWORK_PROTOCOL_VERSION,
-                SemanticAttributes.URL_SCHEME));
+                NetworkAttributes.NETWORK_PROTOCOL_NAME,
+                NetworkAttributes.NETWORK_PROTOCOL_VERSION,
+                UrlAttributes.URL_SCHEME));
   }
 
   private HttpMetricsAdvice() {}

src/main/java/bio/terra/common/opentelemetry/OpenTelemetryConfig.java

@@ -1,7 +1,6 @@
 package bio.terra.common.opentelemetry;
 
 import bio.terra.common.tracing.ExcludingUrlSampler;
-import io.opentelemetry.instrumentation.spring.autoconfigure.EnableOpenTelemetry;
 import io.opentelemetry.sdk.autoconfigure.spi.AutoConfigurationCustomizerProvider;
 import io.opentelemetry.sdk.metrics.InstrumentSelector;
 import io.opentelemetry.sdk.metrics.View;
@@ -18,7 +17,6 @@
 import org.springframework.data.util.Pair;
 
 @Configuration
-@EnableOpenTelemetry
 @EnableConfigurationProperties(value = {TracingProperties.class})
 public class OpenTelemetryConfig {
 

src/main/java/bio/terra/common/tracing/ExcludingUrlSampler.java

@@ -6,7 +6,7 @@
 import io.opentelemetry.sdk.trace.data.LinkData;
 import io.opentelemetry.sdk.trace.samplers.Sampler;
 import io.opentelemetry.sdk.trace.samplers.SamplingResult;
-import io.opentelemetry.semconv.SemanticAttributes;
+import io.opentelemetry.semconv.UrlAttributes;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
@@ -38,8 +38,8 @@ public SamplingResult shouldSample(
     // HTTP_TARGET seems to have the right information but that is deprecated
     // check URL_PATH to be forward compatible. JUST CHECK THEM ALL
     var urlCandidates = new HashSet<String>();
-    urlCandidates.add(attributes.get(SemanticAttributes.URL_PATH));
-    urlCandidates.add(attributes.get(SemanticAttributes.HTTP_TARGET));
+    urlCandidates.add(attributes.get(UrlAttributes.URL_PATH));
+    urlCandidates.add(attributes.get(UrlAttributes.URL_QUERY));
     urlCandidates.add(name);
     // removeAll below does not like nulls so remove any if they exist
     urlCandidates.remove(null);

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

@@ -28,20 +28,20 @@
 @ActiveProfiles("human-readable-logging")
 @Tag("unit")
 @ExtendWith(OutputCaptureExtension.class)
-public class HumanReadableLoggingTest {
+class HumanReadableLoggingTest {
 
   @Autowired private TestRestTemplate testRestTemplate;
   // Spy bean to allow us to mock out the RequestIdFilter ID generator.
   @SpyBean private RequestIdFilter requestIdFilter;
 
   @BeforeEach
-  public void setUp() {
+  void setUp() {
     // Ensure the request ID is always set to a known value.
     when(requestIdFilter.generateRequestId()).thenReturn("12345");
   }
 
   @Test
-  public void testRequestLogging(CapturedOutput capturedOutput) {
+  void testRequestLogging(CapturedOutput capturedOutput) {
     ResponseEntity<String> response =
         testRestTemplate.getForEntity("/testRequestLogging", String.class);
     assertThat(response.getStatusCode().value()).isEqualTo(200);
@@ -55,6 +55,6 @@ public void testRequestLogging(CapturedOutput capturedOutput) {
     // in the main logback.xml
     assertThat(allOutput).contains("12345");
     // Poor-man's check for lack of JSON
-    assertThat(allOutput).doesNotContain("{");
+    assertThat(allOutput).doesNotContain("{\"timestampSeconds\":");
   }
 }

src/test/java/bio/terra/common/tracing/ExcludingUrlSamplerTest.java

@@ -7,17 +7,17 @@
 import io.opentelemetry.context.Context;
 import io.opentelemetry.sdk.trace.samplers.Sampler;
 import io.opentelemetry.sdk.trace.samplers.SamplingDecision;
-import io.opentelemetry.semconv.SemanticAttributes;
+import io.opentelemetry.semconv.UrlAttributes;
 import java.util.List;
 import java.util.Set;
 import org.hamcrest.Matchers;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 
 @Tag("unit")
-public class ExcludingUrlSamplerTest {
+class ExcludingUrlSamplerTest {
   @Test
-  public void testShouldSample() {
+  void testShouldSample() {
     var sampler = new ExcludingUrlSampler(Set.of("/foo", "/bar"), Sampler.alwaysOn());
     assertThat(
         sampler
@@ -28,7 +28,7 @@ public void testShouldSample() {
   }
 
   @Test
-  public void testShouldNotSampleBecauseDelegateSaidDrop() {
+  void testShouldNotSampleBecauseDelegateSaidDrop() {
     var sampler = new ExcludingUrlSampler(Set.of("/foo", "/bar"), Sampler.alwaysOff());
     assertThat(
         sampler
@@ -39,7 +39,7 @@ public void testShouldNotSampleBecauseDelegateSaidDrop() {
   }
 
   @Test
-  public void testShouldNotSampleByName() {
+  void testShouldNotSampleByName() {
     var sampler = new ExcludingUrlSampler(Set.of("/foo", "/bar"), Sampler.alwaysOn());
     assertThat(
         sampler
@@ -50,7 +50,7 @@ public void testShouldNotSampleByName() {
   }
 
   @Test
-  public void testShouldNotSampleByUrlPath() {
+  void testShouldNotSampleByUrlPath() {
     // note that the internal implementation of ExcludingUrlSampler has slightly different behavior
     // when the size of the excludedUrls is smaller than the size of the urlCandidates. So this test
     // has only one excludedUrl to make sure the scenario works. The different behavior comes from
@@ -63,14 +63,14 @@ public void testShouldNotSampleByUrlPath() {
                 "",
                 "/baz",
                 SpanKind.INTERNAL,
-                Attributes.of(SemanticAttributes.URL_PATH, "/bar"),
+                Attributes.of(UrlAttributes.URL_PATH, "/bar"),
                 List.of())
             .getDecision(),
         Matchers.is(SamplingDecision.DROP));
   }
 
   @Test
-  public void testShouldNotSampleByHttpTarget() {
+  void testShouldNotSampleByUrlQuery() {
     var sampler = new ExcludingUrlSampler(Set.of("/foo", "/bar"), Sampler.alwaysOn());
     assertThat(
         sampler
@@ -79,7 +79,7 @@ public void testShouldNotSampleByHttpTarget() {
                 "",
                 "/baz",
                 SpanKind.INTERNAL,
-                Attributes.of(SemanticAttributes.HTTP_TARGET, "/bar"),
+                Attributes.of(UrlAttributes.URL_QUERY, "/bar"),
                 List.of())
             .getDecision(),
         Matchers.is(SamplingDecision.DROP));