Scala 2.13 [CROM-6036] (broadinstitute#6724)

* wip * wip * wip * wip * checkpoint * wip * wip * wip * wip * wip * compiles??? * cleanup * grrr * fix test * fix test * fix bug in choosing default language factory * fix tests * sheesh * oops * some test fixes, some commenting out * fix ordering * forcing with some [force ci] * temporarily comment out more problematic varargs stuff * fix test * why do I have to do [force ci] to get most sub-builds to run? * wip, varargs broken * yaass * checkpoint * checkpoint [force ci] * more [force ci] * restore comment * grrr * grrr [force ci] * cleanup * debug attempt * force debug * grrr * restructure * fixy fix? * cleanup * oops * Revert "debug attempt" This reverts commit 59b4e01. * Revert "force debug" This reverts commit 6b1fba2. * sweepy sweep * try * more * wip * docs * Scala 2.13 codegen fixes * oops * PR feedback * PR feedback * PR feedback * CI bump * Poke CI * Unpoke CI Co-authored-by: Janet Gainer-Dewar <[email protected]>
takeshi-yoshimura · Apr 13, 2022 · a69d12e · a69d12e
1 parent 0bb86b9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Cromwell Change Log
 
+## 79 Release Notes
+
+### Scala 2.13
+
+Cromwell is now built with Scala version 2.13. This change should not be noticeable to users but may be of interest to developers of Cromwell backend implementations.
+
 ## 75 Release Notes
 
 ### New `AwaitingCloudQuota` backend status

diff --git a/CromIAM/src/main/scala/cromiam/server/CromIamServer.scala b/CromIAM/src/main/scala/cromiam/server/CromIamServer.scala
@@ -46,7 +46,7 @@ object CromIamServer extends HttpApp with CromIamApiService with SwaggerService
 
   override val routes: Route = allRoutes ~ swaggerUiResourceRoute
 
-  override val statusService: StatusService = new StatusService(() => Map(Cromwell -> cromwellClient.subsystemStatus, Sam -> samClient.subsystemStatus))
+  override val statusService: StatusService = new StatusService(() => Map(Cromwell -> cromwellClient.subsystemStatus(), Sam -> samClient.subsystemStatus()))
 
   // Override default shutdownsignal which was just "hit return/enter"
   override def waitForShutdownSignal(actorSystem: ActorSystem)(implicit executionContext: ExecutionContext): Future[Done] = {

diff --git a/CromIAM/src/main/scala/cromiam/server/config/CromIamServerConfig.scala b/CromIAM/src/main/scala/cromiam/server/config/CromIamServerConfig.scala
@@ -9,7 +9,7 @@ import common.validation.Validation._
 import cromiam.server.config.CromIamServerConfig._
 import net.ceedubs.ficus.Ficus._
 
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 import scala.util.{Failure, Success, Try}
 
 final case class CromIamServerConfig(cromIamConfig: CromIamConfig,

diff --git a/CromIAM/src/main/scala/cromiam/server/status/StatusCheckedSubsystem.scala b/CromIAM/src/main/scala/cromiam/server/status/StatusCheckedSubsystem.scala
@@ -19,7 +19,7 @@ trait StatusCheckedSubsystem {
     * error messages, otherwise OK = false and include the response body
     */
   def subsystemStatus()(implicit ec: ExecutionContext): Future[SubsystemStatus] = {
-    sttp.get(statusUri).send map { x =>
+    sttp.get(statusUri).send() map { x =>
       x.body match {
         case Right(_) => SubsystemStatus(true, None)
         case Left(errors) => SubsystemStatus(false, Option(List(errors)))

diff --git a/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala b/CromIAM/src/main/scala/cromiam/webservice/QuerySupport.scala
@@ -1,6 +1,7 @@
 package cromiam.webservice
 
 import akka.event.LoggingAdapter
+import akka.http.scaladsl.model.Uri.Query
 import akka.http.scaladsl.model._
 import akka.http.scaladsl.server.Directives._
 import akka.http.scaladsl.server._
@@ -86,7 +87,7 @@ trait QuerySupport extends RequestSupport {
       // DO NOT REMOVE THE NEXT LINE WITHOUT READING THE SCALADOC ON ensureNoLabelOrs
       ensureNoLabelOrs(user, labelOrs)
 
-      val newQueryBuilder = query.newBuilder
+      val newQueryBuilder = Query.newBuilder
       newQueryBuilder ++= query
 
       val collectionLabels = userCollectionLabels(user, collections)

diff --git a/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala b/CromIAM/src/main/scala/cromiam/webservice/SubmissionSupport.scala
@@ -109,7 +109,7 @@ object SubmissionSupport {
   }
 
   def extractInputAux: Directive1[Map[String, String]] = {
-    formFieldMap.map(_.filterKeys(_.startsWith(WorkflowInputsAuxPrefix)))
+    formFieldMap.map(_.view.filterKeys(_.startsWith(WorkflowInputsAuxPrefix)).toMap)
   }
 
   // FIXME: Much like CromwellClient see if there are ways of unifying this a bit w/ the mothership

diff --git a/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala b/CromIAM/src/test/scala/cromiam/webservice/SwaggerServiceSpec.scala
@@ -14,7 +14,7 @@ import org.yaml.snakeyaml.error.YAMLException
 import org.yaml.snakeyaml.nodes.MappingNode
 import org.yaml.snakeyaml.{Yaml => SnakeYaml}
 
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 
 
 class SwaggerServiceSpec extends AnyFlatSpec with CromwellTimeoutSpec with SwaggerService with ScalatestRouteTest with Matchers

diff --git a/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala b/backend/src/main/scala/cromwell/backend/BackendLifecycleActor.scala
@@ -40,7 +40,7 @@ trait BackendLifecycleActor extends Actor {
   protected def performActionThenRespond(operation: => Future[BackendWorkflowLifecycleActorResponse],
                                          onFailure: Throwable => BackendWorkflowLifecycleActorResponse,
                                          andThen: => Unit = ()) = {
-    val respondTo: ActorRef = sender
+    val respondTo: ActorRef = sender()
     operation onComplete {
       case Success(r) =>
         respondTo ! r

diff --git a/backend/src/main/scala/cromwell/backend/BackendWorkflowFinalizationActor.scala b/backend/src/main/scala/cromwell/backend/BackendWorkflowFinalizationActor.scala
@@ -28,7 +28,7 @@ object BackendWorkflowFinalizationActor {
 trait BackendWorkflowFinalizationActor extends BackendWorkflowLifecycleActor with ActorLogging {
 
   def receive: Receive = LoggingReceive {
-    case Finalize => performActionThenRespond(afterAll map { _ => FinalizationSuccess }, onFailure = FinalizationFailed)
+    case Finalize => performActionThenRespond(afterAll() map { _ => FinalizationSuccess }, onFailure = FinalizationFailed)
   }
 
   /**

diff --git a/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala b/backend/src/main/scala/cromwell/backend/OutputEvaluator.scala
@@ -78,7 +78,7 @@ object OutputEvaluator {
       case Success(Invalid(errors)) => InvalidJobOutputs(errors)
       case Failure(exception) => JobOutputsEvaluationException(exception)
     }
-    
+
     /*
       * Because Cromwell doesn't trust anyone, if custom evaluation is provided,
       * still make sure that all the output ports have been filled with values
@@ -90,7 +90,7 @@ object OutputEvaluator {
         case Nil =>
           val errorMessagePrefix = "Error applying postMapper in short-circuit output evaluation"
           TryUtil.sequenceMap(outputs map { case (k, v) => (k, postMapper(v))}, errorMessagePrefix) match {
-            case Failure(e) => InvalidJobOutputs(NonEmptyList.of(e.getMessage, e.getStackTrace.take(5).map(_.toString):_*))
+            case Failure(e) => InvalidJobOutputs(NonEmptyList.of(e.getMessage, e.getStackTrace.take(5).toIndexedSeq.map(_.toString):_*))
             case Success(postMappedOutputs) => ValidJobOutputs(CallOutputs(postMappedOutputs))
           }
         case head :: tail => InvalidJobOutputs(NonEmptyList.of(toError(head), tail.map(toError): _*))

diff --git a/backend/src/main/scala/cromwell/backend/dummy/DummyInitializationActor.scala b/backend/src/main/scala/cromwell/backend/dummy/DummyInitializationActor.scala
@@ -17,7 +17,7 @@ class DummyInitializationActor(pipelinesParams: StandardInitializationActorParam
   val backendAttributeValidation: RuntimeAttributesValidation[String] = new RuntimeAttributesValidation[String] {
     override def key: String = "backend"
 
-    override def coercion: Traversable[WomType] = Vector(WomStringType)
+    override def coercion: Iterable[WomType] = Vector(WomStringType)
 
     override protected def validateValue: PartialFunction[WomValue, ErrorOr[String]] = {
       case WomString("Dummy") => "Dummy".validNel

diff --git a/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala b/backend/src/main/scala/cromwell/backend/standard/StandardAsyncExecutionActor.scala
@@ -250,7 +250,7 @@ trait StandardAsyncExecutionActor
     * @param directoryFiles The directories.
     * @return The shell scripting.
     */
-  def directoryScripts(directoryFiles: Traversable[WomUnlistedDirectory]): String =
+  def directoryScripts(directoryFiles: Iterable[WomUnlistedDirectory]): String =
     directoryFiles map directoryScript mkString "\n"
 
   /**
@@ -284,7 +284,7 @@ trait StandardAsyncExecutionActor
     * @param globFiles The globs.
     * @return The shell scripting.
     */
-  def globScripts(globFiles: Traversable[WomGlobFile]): String =
+  def globScripts(globFiles: Iterable[WomGlobFile]): String =
     globFiles map globScript mkString "\n"
 
   /**
@@ -549,6 +549,7 @@ trait StandardAsyncExecutionActor
       CommandSetupSideEffectFile(womValue, alternativeName)
     case AsLocalizedAdHocValue(LocalizedAdHocValue(AdHocValue(womValue, alternativeName, _), _)) =>
       CommandSetupSideEffectFile(womValue, alternativeName)
+    case oh => throw new Exception(s"Programmer Error! Unexpected case match: $oh")
   }
 
   lazy val evaluatedAdHocFiles: ErrorOr[List[AdHocValue]] = {
@@ -986,7 +987,7 @@ trait StandardAsyncExecutionActor
       case InvalidJobOutputs(errors) =>
         val exception = new MessageAggregation {
           override def exceptionContext: String = "Failed to evaluate job outputs"
-          override def errorMessages: Traversable[String] = errors.toList
+          override def errorMessages: Iterable[String] = errors.toList
         }
         FailedNonRetryableExecutionHandle(exception, kvPairsToSave = None)
       case JobOutputsEvaluationException(exception: Exception) if retryEvaluateOutputsAggregated(exception) =>
@@ -1068,7 +1069,7 @@ trait StandardAsyncExecutionActor
       Map(key -> nextKvPair)
     }
 
-    val kvsFromPreviousAttemptUpd = kvsFromPreviousAttempt.mapValues(kvPair => kvPair.copy(key = kvPair.key.copy(jobKey = nextKvJobKey)))
+    val kvsFromPreviousAttemptUpd = kvsFromPreviousAttempt.view.mapValues(kvPair => kvPair.copy(key = kvPair.key.copy(jobKey = nextKvJobKey)))
 
     val failedRetryCountKvPair: Map[String, KvPair] =
       if (incrementFailedRetryCount) getNextKvPair(FailedRetryCountKey, (previousFailedRetries + 1).toString)
@@ -1081,7 +1082,7 @@ trait StandardAsyncExecutionActor
 
     val mergedKvs = kvsFromPreviousAttemptUpd ++ kvsForNextAttempt ++ failedRetryCountKvPair ++ memoryMultiplierKvPair
 
-    makeKvRequest(mergedKvs.values.map(KvPut).toSeq) map { respSeq =>
+    makeKvRequest(mergedKvs.toMap.values.map(KvPut).toSeq) map { respSeq =>
       val failures = respSeq.filter(_.isInstanceOf[KvFailure])
       if (failures.isEmpty) {
         respSeq

diff --git a/...src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala b/...src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala
@@ -36,7 +36,7 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
     // Hash Request
     case hashCommand: IoHashCommandWithContext =>
       val key = hashCommand.fileHashContext.file
-      lazy val requester = FileHashRequester(sender, hashCommand.fileHashContext, hashCommand.ioHashCommand)
+      lazy val requester = FileHashRequester(sender(), hashCommand.fileHashContext, hashCommand.ioHashCommand)
       cache.get(key) match {
         case FileHashValueNotRequested =>
           // The hash is not in the cache and has not been requested. Make the hash request and register this requester
@@ -48,9 +48,9 @@ class RootWorkflowFileHashCacheActor private[callcaching](override val ioActor:
           // hash to become available.
           cache.put(key, FileHashValueRequested(requesters = requester :: requesters))
         case FileHashSuccess(value) =>
-          sender ! Tuple2(hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
+          sender() ! Tuple2(hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
         case FileHashFailure(error) =>
-          sender ! Tuple2(hashCommand.fileHashContext, IoFailure(requester.ioCommand, new IOException(error)))
+          sender() ! Tuple2(hashCommand.fileHashContext, IoFailure(requester.ioCommand, new IOException(error)))
       }
     // Hash Success
     case (hashContext: FileHashContext, success @ IoSuccess(_, value: String)) =>

diff --git a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesDefault.scala b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesDefault.scala
@@ -12,7 +12,7 @@ import scala.util.{Failure, Try}
 
 object RuntimeAttributesDefault {
 
-  def workflowOptionsDefault(options: WorkflowOptions, mapping: Map[String, Traversable[WomType]]):
+  def workflowOptionsDefault(options: WorkflowOptions, mapping: Map[String, Iterable[WomType]]):
   Try[Map[String, WomValue]] = {
     options.defaultRuntimeOptions flatMap { attrs =>
       TryUtil.sequenceMap(attrs collect {
@@ -32,7 +32,7 @@ object RuntimeAttributesDefault {
    */
   def withDefaults(attrs: EvaluatedRuntimeAttributes, defaultsList: List[EvaluatedRuntimeAttributes]): EvaluatedRuntimeAttributes = {
     defaultsList.foldLeft(attrs)((acc, default) => {
-      acc ++ default.filterKeys(!acc.keySet.contains(_))
+      acc ++ default.view.filterKeys(!acc.keySet.contains(_))
     })
   }
 

diff --git a/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala b/backend/src/main/scala/cromwell/backend/validation/RuntimeAttributesValidation.scala
@@ -84,7 +84,7 @@ object RuntimeAttributesValidation {
     new RuntimeAttributesValidation[ValidatedType] {
       override def key: String = validation.key
 
-      override def coercion: Traversable[WomType] = validation.coercion
+      override def coercion: Iterable[WomType] = validation.coercion
 
       override protected def validateValue: PartialFunction[WomValue, ErrorOr[ValidatedType]] =
         validation.validateValuePackagePrivate
@@ -108,7 +108,7 @@ object RuntimeAttributesValidation {
     new RuntimeAttributesValidation[ValidatedType] {
       override def key: String = validation.key
 
-      override def coercion: Traversable[WomType] = validation.coercion
+      override def coercion: Iterable[WomType] = validation.coercion
 
       override protected def validateValue: PartialFunction[WomValue, ErrorOr[ValidatedType]] =
         validation.validateValuePackagePrivate
@@ -132,7 +132,7 @@ object RuntimeAttributesValidation {
     new OptionalRuntimeAttributesValidation[ValidatedType] {
       override def key: String = validation.key
 
-      override def coercion: Traversable[WomType] = validation.coercion
+      override def coercion: Iterable[WomType] = validation.coercion
 
       override protected def validateOption: PartialFunction[WomValue, ErrorOr[ValidatedType]] =
         validation.validateValuePackagePrivate
@@ -162,7 +162,7 @@ object RuntimeAttributesValidation {
     val attributeOptions: Map[String, Option[Any]] = validatedRuntimeAttributes.attributes.safeMapValues(unpackOption)
 
     val attributes: Map[String, String] = attributeOptions collect {
-      case (name, Some(values: Traversable[_])) => (name, values.mkString(","))
+      case (name, Some(values: Iterable[_])) => (name, values.mkString(","))
       case (name, Some(value)) => (name, value.toString)
     }
 
@@ -271,7 +271,7 @@ trait RuntimeAttributesValidation[ValidatedType] {
     *
     * @return traversable of wdl types
     */
-  def coercion: Traversable[WomType]
+  def coercion: Iterable[WomType]
 
   /**
     * Validates the wdl value.

diff --git a/backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala b/backend/src/main/scala/cromwell/backend/validation/ValidatedRuntimeAttributesBuilder.scala
@@ -47,7 +47,7 @@ trait ValidatedRuntimeAttributesBuilder {
   /**
     * Returns a map of coercions suitable for RuntimeAttributesDefault.workflowOptionsDefault.
     */
-  final lazy val coercionMap: Map[String, Traversable[WomType]] = {
+  final lazy val coercionMap: Map[String, Iterable[WomType]] = {
     validations.map(validation => validation.key -> validation.coercion).toMap
   }
 
@@ -64,7 +64,7 @@ trait ValidatedRuntimeAttributesBuilder {
       case Invalid(nel) => throw new RuntimeException with MessageAggregation with NoStackTrace {
         override def exceptionContext: String = "Runtime attribute validation failed"
 
-        override def errorMessages: Traversable[String] = nel.toList
+        override def errorMessages: Iterable[String] = nel.toList
       }
     }
   }

diff --git a/.../src/main/scala/cromwell/backend/validation/exception/ValidationAggregatedException.scala b/.../src/main/scala/cromwell/backend/validation/exception/ValidationAggregatedException.scala
@@ -3,4 +3,4 @@ package cromwell.backend.validation.exception
 import common.exception.MessageAggregation
 
 case class ValidationAggregatedException(override val exceptionContext: String,
-                                         override val errorMessages: Traversable[String]) extends MessageAggregation
+                                         override val errorMessages: Iterable[String]) extends MessageAggregation
diff --git a/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala b/backend/src/test/scala/cromwell/backend/BackendWorkflowInitializationActorSpec.scala
@@ -79,7 +79,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.right.get should be(ContinueOnReturnCodeFlag(value))
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeFlag(value))
     }
 
     forAll(booleanRows) { value =>
@@ -90,7 +90,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.right.get should be(ContinueOnReturnCodeFlag(value))
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeFlag(value))
     }
 
     forAll(booleanRows) { value =>
@@ -109,7 +109,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.right.get should be(ContinueOnReturnCodeSet(Set(value)))
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
 
     forAll(integerRows) { value =>
@@ -120,7 +120,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.right.get should be(ContinueOnReturnCodeSet(Set(value)))
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
 
     forAll(integerRows) { value =>
@@ -139,7 +139,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.right.get should be(ContinueOnReturnCodeSet(Set(value)))
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
 
     forAll(integerRows) { value =>
@@ -150,7 +150,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.right.get should be(ContinueOnReturnCodeSet(Set(value)))
+      valid.toEither.toOption.get should be(ContinueOnReturnCodeSet(Set(value)))
     }
 
     forAll(integerRows) { value =>
@@ -176,7 +176,7 @@ class BackendWorkflowInitializationActorSpec extends TestKitSuite
       val valid =
         ContinueOnReturnCodeValidation.default(optionalConfig).validate(Map(RuntimeAttributesKeys.ContinueOnReturnCodeKey -> womValue))
       valid.isValid should be(result)
-      valid.toEither.left.get.toList should contain theSameElementsAs List(
+      valid.toEither.swap.toOption.get.toList should contain theSameElementsAs List(
         "Expecting continueOnReturnCode runtime attribute to be either a Boolean, a String 'true' or 'false', or an Array[Int]"
       )
     }

diff --git a/.../test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala b/.../test/scala/cromwell/backend/standard/StandardValidatedRuntimeAttributesBuilderSpec.scala
@@ -71,7 +71,7 @@ class StandardValidatedRuntimeAttributesBuilderSpec extends AnyWordSpecLike with
       val runtimeAttributes = Map("docker" -> WomString("ubuntu:latest"))
       var warnings = List.empty[Any]
       val mockLogger = mock[Logger]
-      mockLogger.warn(anyString).answers(warnings :+= _)
+      mockLogger.warn(anyString).answers((warnings :+= _): Any => Unit)
       assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,
         includeDockerSupport = false, logger = mockLogger)
       warnings should contain theSameElementsAs List("Unrecognized runtime attribute keys: docker")
@@ -93,7 +93,7 @@ class StandardValidatedRuntimeAttributesBuilderSpec extends AnyWordSpecLike with
       val runtimeAttributes = Map("docker" -> WomInteger(1))
       var warnings = List.empty[Any]
       val mockLogger = mock[Logger]
-      mockLogger.warn(anyString).answers(warnings :+= _)
+      mockLogger.warn(anyString).answers((warnings :+= _): Any => Unit)
       assertRuntimeAttributesSuccessfulCreation(runtimeAttributes, expectedRuntimeAttributes,
         includeDockerSupport = false, logger = mockLogger)
       warnings should contain theSameElementsAs List("Unrecognized runtime attribute keys: docker")

diff --git a/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala b/backend/src/test/scala/cromwell/backend/validation/RuntimeAttributesValidationSpec.scala
@@ -368,7 +368,7 @@ class RuntimeAttributesValidationSpec extends AnyWordSpecLike with CromwellTimeo
            |continueOnReturnCode = [0,1,2]
            |""".stripMargin))
 
-      ContinueOnReturnCodeValidation.configDefaultWdlValue(optinalBackendConfig).get shouldBe WomArray(WomArrayType(WomIntegerType), Array(WomInteger(0), WomInteger(1), WomInteger(2)))
+      ContinueOnReturnCodeValidation.configDefaultWdlValue(optinalBackendConfig).get shouldBe WomArray(WomArrayType(WomIntegerType), List(WomInteger(0), WomInteger(1), WomInteger(2)))
     }
 
     "return failure when tries to validate an invalid maxRetries entry" in {

diff --git a/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala b/centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala
@@ -24,7 +24,7 @@ import net.ceedubs.ficus.Ficus._
 import org.apache.commons.lang3.exception.ExceptionUtils
 import org.threeten.bp.Duration
 
-import scala.collection.JavaConverters._
+import scala.jdk.CollectionConverters._
 import scala.concurrent.ExecutionContext
 
 class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorReporter {