[WOR-1560] Upgrade to TCL 1.0.10 for MDC-aware Stairway (#424)

buildSrc/src/main/groovy/bio.terra.landingzone.java-common-conventions.gradle

@@ -42,23 +42,18 @@ dependencies {
     compileOnly "com.google.code.findbugs:annotations:3.0.1"
     implementation 'org.slf4j:slf4j-api'
     implementation 'io.swagger.core.v3:swagger-annotations:2.1.12'
+    implementation 'io.opentelemetry.instrumentation:opentelemetry-instrumentation-annotations:2.2.0'
+    // Needed for @VisibleForTesting and more:
+    // TCL 1.0.10 tries to expose this as an api dependency, but does so without specifying an explicit version
+    // (it derives the version from com.google.cloud:libraries-bom, which it doesn't expose to consumers).
+    // If TCL instead exposed the BOM, or exposed guava with a specified version, this could be removed.
+    implementation 'com.google.guava:guava:33.1.0-jre'
     swaggerCodegen 'io.swagger.codegen.v3:swagger-codegen-cli:3.0.47'
 
     testImplementation 'ch.qos.logback:logback-classic'
     testImplementation 'org.hamcrest:hamcrest:2.2'
 
-    var openTelemetryVersion = '1.32.0'
-    implementation "io.opentelemetry:opentelemetry-api:${openTelemetryVersion}"
-    implementation "io.opentelemetry:opentelemetry-sdk:${openTelemetryVersion}"
-    implementation "io.opentelemetry:opentelemetry-sdk-metrics:${openTelemetryVersion}"
-    implementation "io.opentelemetry:opentelemetry-exporter-logging:${openTelemetryVersion}"
-    implementation "io.opentelemetry.semconv:opentelemetry-semconv:1.21.0-alpha"
-    implementation "io.opentelemetry.instrumentation:opentelemetry-spring-webmvc-6.0:${openTelemetryVersion}-alpha"
-    implementation "io.opentelemetry.instrumentation:opentelemetry-instrumentation-annotations:${openTelemetryVersion}"
-    implementation "io.opentelemetry.instrumentation:opentelemetry-spring-boot:${openTelemetryVersion}-alpha"
-    implementation "com.google.cloud.opentelemetry:exporter-trace:0.25.2"
-
-    implementation ('bio.terra:terra-common-lib:0.1.6-SNAPSHOT'){
+    implementation ('bio.terra:terra-common-lib:1.0.10-SNAPSHOT') {
         exclude group: "org.broadinstitute.dsde.workbench", module: "sam-client_2.13"
     }
 }

buildSrc/src/main/groovy/bio.terra.landingzone.java-spring-app-conventions.gradle

@@ -1,9 +1,4 @@
 plugins {
-    id 'bio.terra.landingzone.java-common-conventions'
-    id 'io.spring.dependency-management'
-    id 'org.springframework.boot'
+    id 'bio.terra.landingzone.java-spring-conventions'
     id 'application'
 }
-
-// Spring Boot 3.1.2 pulls in postgresql 42.6.0, vulnerable to CVE-2024-1597
-ext['postgresql.version'] = '42.7.2'

buildSrc/src/main/groovy/bio.terra.landingzone.java-spring-conventions.gradle

@@ -0,0 +1,11 @@
+plugins {
+    id 'bio.terra.landingzone.java-common-conventions'
+    id 'io.spring.dependency-management'
+    id 'org.springframework.boot'
+}
+
+// Spring Boot 3.1.2 pulls in postgresql 42.6.0, vulnerable to CVE-2024-1597
+ext['postgresql.version'] = '42.7.2'
+// Spring Boot 3.1.2 pulls in opentelemetry-bom 1.25.0.
+// It must have version >= 1.34.1 for compatibility with terra-common-lib 1.0.9:
+ext['opentelemetry.version'] = '1.36.0'

buildSrc/src/main/groovy/bio.terra.landingzone.java-spring-library-conventions.gradle

@@ -1,7 +1,5 @@
 plugins {
-    id 'bio.terra.landingzone.java-common-conventions'
-    id 'io.spring.dependency-management'
-    id 'org.springframework.boot'
+    id 'bio.terra.landingzone.java-spring-conventions'
     id 'java-library'
     id 'maven-publish'
 }

library/build.gradle

@@ -11,7 +11,6 @@ plugins {
 apply from: 'publishing.gradle'
 
 dependencies {
-    implementation 'bio.terra:terra-common-lib'
     implementation 'org.apache.commons:commons-dbcp2'
     implementation 'org.springframework.boot:spring-boot-starter-data-jdbc'
     implementation 'org.springframework.boot:spring-boot-starter-web'
@@ -57,7 +56,7 @@ dependencies {
 
     testImplementation 'org.mockito:mockito-inline:5.2.0'
     testImplementation 'org.awaitility:awaitility:4.2.0'
-    testImplementation('org.springframework.boot:spring-boot-starter-test:3.1.2') {
+    testImplementation('org.springframework.boot:spring-boot-starter-test') {
         // Fixes warning about multiple occurrences of JSONObject on the classpath
         exclude group: 'com.vaadin.external.google', module: 'android-json'
     }

library/src/main/java/bio/terra/landingzone/job/LandingZoneJobBuilder.java

@@ -8,7 +8,6 @@
 import bio.terra.landingzone.job.exception.InvalidJobParameterException;
 import bio.terra.landingzone.job.model.OperationType;
 import bio.terra.landingzone.service.landingzone.azure.model.LandingZoneRequest;
-import bio.terra.landingzone.stairway.common.utils.LandingZoneMdcHook;
 import bio.terra.landingzone.stairway.flight.LandingZoneFlightMapKeys;
 import bio.terra.stairway.Flight;
 import bio.terra.stairway.FlightMap;
@@ -20,7 +19,6 @@
 public class LandingZoneJobBuilder {
   private final LandingZoneJobService jobService;
   private final StairwayComponent stairwayComponent;
-  private final LandingZoneMdcHook mdcHook;
   private final FlightMap jobParameterMap;
   private final OpenTelemetry openTelemetry;
   private Class<? extends Flight> flightClass;
@@ -33,11 +31,9 @@ public class LandingZoneJobBuilder {
   public LandingZoneJobBuilder(
       LandingZoneJobService jobService,
       StairwayComponent stairwayComponent,
-      LandingZoneMdcHook mdcHook,
       OpenTelemetry openTelemetry) {
     this.jobService = jobService;
     this.stairwayComponent = stairwayComponent;
-    this.mdcHook = mdcHook;
     this.openTelemetry = openTelemetry;
     this.jobParameterMap = new FlightMap();
   }
@@ -126,8 +122,7 @@ private void populateInputParams() {
       jobId = stairwayComponent.get().createFlightId();
     }
 
-    // Always add the MDC logging and tracing span parameters for the mdc hook
-    addParameter(LandingZoneMdcHook.MDC_FLIGHT_MAP_KEY, mdcHook.getSerializedCurrentContext());
+    // Always add the tracing span parameters
     addParameter(
         MonitoringHook.SUBMISSION_SPAN_CONTEXT_MAP_KEY,
         MonitoringHook.serializeCurrentTracingContext(openTelemetry));

library/src/main/java/bio/terra/landingzone/job/LandingZoneJobService.java

@@ -27,7 +27,7 @@
 import bio.terra.landingzone.service.iam.SamRethrow;
 import bio.terra.landingzone.service.landingzone.azure.model.DeletedLandingZone;
 import bio.terra.landingzone.service.landingzone.azure.model.LandingZoneRequest;
-import bio.terra.landingzone.stairway.common.utils.LandingZoneMdcHook;
+import bio.terra.landingzone.stairway.common.utils.StairwayLoggingHook;
 import bio.terra.landingzone.stairway.flight.LandingZoneFlightMapKeys;
 import bio.terra.stairway.Flight;
 import bio.terra.stairway.FlightDebugInfo;
@@ -68,7 +68,7 @@ public class LandingZoneJobService {
   private final LandingZoneIngressConfiguration ingressConfig;
   private final LandingZoneStairwayDatabaseConfiguration stairwayDatabaseConfiguration;
   private final ScheduledExecutorService executor;
-  private final LandingZoneMdcHook mdcHook;
+  private final StairwayLoggingHook stairwayLoggingHook;
   private final StairwayComponent stairwayComponent;
   private final LandingZoneFlightBeanBag flightBeanBag;
   private final ObjectMapper objectMapper;
@@ -81,7 +81,7 @@ public LandingZoneJobService(
       LandingZoneJobConfiguration jobConfig,
       LandingZoneIngressConfiguration ingressConfig,
       LandingZoneStairwayDatabaseConfiguration stairwayDatabaseConfiguration,
-      LandingZoneMdcHook mdcHook,
+      StairwayLoggingHook stairwayLoggingHook,
       @Qualifier("landingZoneStairwayComponent") StairwayComponent stairwayComponent,
       LandingZoneFlightBeanBag flightBeanBag,
       ObjectMapper objectMapper,
@@ -91,7 +91,7 @@ public LandingZoneJobService(
     this.ingressConfig = ingressConfig;
     this.stairwayDatabaseConfiguration = stairwayDatabaseConfiguration;
     this.executor = Executors.newScheduledThreadPool(jobConfig.getMaxThreads());
-    this.mdcHook = mdcHook;
+    this.stairwayLoggingHook = stairwayLoggingHook;
     this.stairwayComponent = stairwayComponent;
     this.flightBeanBag = flightBeanBag;
     this.objectMapper = objectMapper;
@@ -101,7 +101,7 @@ public LandingZoneJobService(
 
   // Fully fluent style of JobBuilder
   public LandingZoneJobBuilder newJob() {
-    return new LandingZoneJobBuilder(this, stairwayComponent, mdcHook, openTelemetry);
+    return new LandingZoneJobBuilder(this, stairwayComponent, openTelemetry);
   }
 
   // submit a new job to stairway
@@ -176,7 +176,7 @@ public void initialize() {
             .newStairwayOptionsBuilder()
             .dataSource(DataSourceInitializer.initializeDataSource(stairwayDatabaseConfiguration))
             .context(flightBeanBag)
-            .addHook(mdcHook)
+            .addHook(stairwayLoggingHook)
             .addHook(new MonitoringHook(openTelemetry))
             .exceptionSerializer(new StairwayExceptionSerializer(objectMapper)));
   }