Update scala-library from 2.13.10 to 2.13.12 (#2540)

Author: broadbot

core/src/main/scala/org/broadinstitute/dsde/rawls/Boot.scala

@@ -95,8 +95,8 @@ object Boot extends IOApp with LazyLogging {
     val gcsConfig = conf.getConfig("gcs")
 
     // we need an ActorSystem to host our application in
-    implicit val system = ActorSystem("rawls")
-    implicit val materializer = ActorMaterializer()
+    implicit val system: ActorSystem = ActorSystem("rawls")
+    implicit val materializer: ActorMaterializer = ActorMaterializer()
 
     val slickDataSource = DataSource(DatabaseConfig.forConfig[JdbcProfile]("slick", conf))
 

core/src/main/scala/org/broadinstitute/dsde/rawls/billing/BillingProfileManagerDAO.scala

@@ -15,7 +15,7 @@ import org.broadinstitute.dsde.rawls.model.{
   RawlsBillingAccountName,
   RawlsRequestContext
 }
-import spray.json.DefaultJsonProtocol
+import spray.json.{DefaultJsonProtocol, RootJsonFormat}
 
 import java.util.{Date, UUID}
 import scala.annotation.tailrec
@@ -26,7 +26,9 @@ import scala.util.{Failure, Success, Try}
 case class BpmAzureReportErrorMessage(message: String, statusCode: Int)
 
 object BpmAzureReportErrorMessageJsonProtocol extends DefaultJsonProtocol {
-  implicit val bpmAzureReportErrorMessageFormat = jsonFormat2(BpmAzureReportErrorMessage.apply)
+  implicit val bpmAzureReportErrorMessageFormat: RootJsonFormat[BpmAzureReportErrorMessage] = jsonFormat2(
+    BpmAzureReportErrorMessage.apply
+  )
 }
 
 import spray.json._

core/src/main/scala/org/broadinstitute/dsde/rawls/billing/BillingProjectOrchestrator.scala

@@ -57,7 +57,7 @@ class BillingProjectOrchestrator(ctx: RawlsRequestContext,
     extends StringValidationUtils
     with UserUtils
     with LazyLogging {
-  implicit val errorReportSource = ErrorReportSource("rawls")
+  implicit val errorReportSource: ErrorReportSource = ErrorReportSource("rawls")
 
   /**
    * Creates a "v2" billing project, using either Azure managed app coordinates or a Google Billing Account

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/GoogleBigQueryServiceFactory.scala

@@ -7,6 +7,7 @@ import org.apache.commons.io.IOUtils
 import org.broadinstitute.dsde.rawls.model.GoogleProjectId
 import org.broadinstitute.dsde.workbench.google2.GoogleBigQueryService
 import org.broadinstitute.dsde.workbench.model.google.GoogleProject
+import org.typelevel.log4cats.SelfAwareStructuredLogger
 import org.typelevel.log4cats.slf4j.Slf4jLogger
 
 import java.io.ByteArrayInputStream
@@ -23,8 +24,8 @@ import scala.concurrent.ExecutionContext
  */
 class GoogleBigQueryServiceFactory(pathToCredentialJson: String)(implicit executionContext: ExecutionContext) {
 
-  implicit lazy val logger = Slf4jLogger.getLogger[IO]
-  implicit lazy val timer = Temporal[IO]
+  implicit lazy val logger: SelfAwareStructuredLogger[IO] = Slf4jLogger.getLogger[IO]
+  implicit lazy val timer: Temporal[IO] = Temporal[IO]
 
   def getServiceForPet(petKey: String,
                        projectId: GoogleProject

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/HttpBondApiDAO.scala

@@ -10,6 +10,7 @@ import org.broadinstitute.dsde.rawls.RawlsExceptionWithErrorReport
 import org.broadinstitute.dsde.rawls.dataaccess.BondJsonSupport._
 import org.broadinstitute.dsde.rawls.model.UserInfo
 import org.broadinstitute.dsde.rawls.util.{HttpClientUtilsStandard, Retry}
+import spray.json.RootJsonFormat
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -21,10 +22,12 @@ case class Providers(providers: List[String])
 object BondJsonSupport {
   import spray.json.DefaultJsonProtocol._
 
-  implicit val BondServiceAccountEmailFormat = jsonFormat1(BondServiceAccountEmail)
-  implicit val BondResponseDataFormat = jsonFormat1(BondResponseData)
+  implicit val BondServiceAccountEmailFormat: RootJsonFormat[BondServiceAccountEmail] = jsonFormat1(
+    BondServiceAccountEmail
+  )
+  implicit val BondResponseDataFormat: RootJsonFormat[BondResponseData] = jsonFormat1(BondResponseData)
 
-  implicit val providersFormat = jsonFormat1(Providers)
+  implicit val providersFormat: RootJsonFormat[Providers] = jsonFormat1(Providers)
 
 }
 

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/HttpExecutionServiceDAO.scala

@@ -1,7 +1,7 @@
 package org.broadinstitute.dsde.rawls.dataaccess
 
 import akka.actor.ActorSystem
-import akka.http.scaladsl.Http
+import akka.http.scaladsl.{Http, HttpExt}
 import akka.http.scaladsl.client.RequestBuilding._
 import akka.http.scaladsl.marshallers.sprayjson.SprayJsonSupport._
 import akka.http.scaladsl.marshalling.Marshal
@@ -16,7 +16,7 @@ import org.broadinstitute.dsde.rawls.metrics.{Expansion, InstrumentedRetry, Rawl
 import org.broadinstitute.dsde.rawls.model.ExecutionJsonSupport._
 import org.broadinstitute.dsde.rawls.model.StatusJsonSupport._
 import org.broadinstitute.dsde.rawls.model._
-import org.broadinstitute.dsde.rawls.util.{FutureSupport, HttpClientUtilsGzipInstrumented}
+import org.broadinstitute.dsde.rawls.util.{FutureSupport, HttpClientUtils, HttpClientUtilsGzipInstrumented}
 import spray.json.DefaultJsonProtocol._
 import spray.json._
 
@@ -38,11 +38,11 @@ class HttpExecutionServiceDAO(executionServiceURL: String, override val workbenc
     with LazyLogging
     with RawlsInstrumented {
 
-  implicit private lazy val baseMetricBuilder =
+  implicit private lazy val baseMetricBuilder: ExpandedMetricBuilder =
     ExpandedMetricBuilder.expand(SubsystemMetricKey, Subsystems.Cromwell)
 
-  override val http = Http(system)
-  override val httpClientUtils = HttpClientUtilsGzipInstrumented()
+  override val http: HttpExt = Http(system)
+  override val httpClientUtils: HttpClientUtils = HttpClientUtilsGzipInstrumented()
 
   // Strip out workflow IDs from metrics by providing a redactedUriExpansion
   override protected val UriExpansion: Expansion[Uri] = RawlsExpansion.redactedUriExpansion(

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/HttpGoogleServicesDAO.scala

@@ -61,6 +61,7 @@ import org.broadinstitute.dsde.workbench.google2.util.RetryPredicates
 import org.broadinstitute.dsde.workbench.model.google.{GcsBucketName, GoogleProject, GoogleResourceTypes, IamPermission}
 import org.broadinstitute.dsde.workbench.model.{TraceId, WorkbenchEmail}
 import org.joda.time.DateTime
+import org.typelevel.log4cats.SelfAwareStructuredLogger
 import org.typelevel.log4cats.slf4j.Slf4jLogger
 import spray.json._
 
@@ -101,7 +102,7 @@ class HttpGoogleServicesDAO(val clientSecrets: GoogleClientSecrets,
     with GoogleUtilities {
   val http = Http(system)
   val httpClientUtils = HttpClientUtilsStandard()
-  implicit val log4CatsLogger = Slf4jLogger.getLogger[IO]
+  implicit val log4CatsLogger: SelfAwareStructuredLogger[IO] = Slf4jLogger.getLogger[IO]
 
   val groupMemberRole =
     "MEMBER" // the Google Group role corresponding to a member (note that this is distinct from the GCS roles defined in WorkspaceAccessLevel)

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/HttpImportServiceDAO.scala

@@ -10,14 +10,15 @@ import org.broadinstitute.dsde.rawls.RawlsExceptionWithErrorReport
 import org.broadinstitute.dsde.rawls.model.ImportStatuses.ImportStatus
 import org.broadinstitute.dsde.rawls.model.{ImportStatuses, UserInfo, WorkspaceName}
 import org.broadinstitute.dsde.rawls.util.{HttpClientUtilsStandard, Retry}
+import spray.json.RootJsonFormat
 
 import java.util.UUID
 import scala.concurrent.{ExecutionContext, Future}
 
 object ImportServiceJsonSupport {
   import spray.json.DefaultJsonProtocol._
 
-  implicit val importServiceResponseFormat = jsonFormat2(ImportServiceResponse)
+  implicit val importServiceResponseFormat: RootJsonFormat[ImportServiceResponse] = jsonFormat2(ImportServiceResponse)
 }
 
 class HttpImportServiceDAO(url: String)(implicit

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/DriverComponent.scala

@@ -16,7 +16,7 @@ trait DriverComponent extends StringValidationUtils {
   val batchSize: Int // used for writes to group inserts/updates; must be explicitly utilized via custom business logic
   val fetchSize: Int // used during Slick streaming to set the size of pages; must be explicitly set via withStatementParameters
   implicit val executionContext: ExecutionContext
-  implicit override val errorReportSource = ErrorReportSource("rawls")
+  implicit override val errorReportSource: ErrorReportSource = ErrorReportSource("rawls")
 
   // needed by MySQL but not actually used; we will always overwrite
   val defaultTimeStamp = Timestamp.valueOf("2001-01-01 01:01:01.0")
@@ -108,8 +108,9 @@ trait RawSqlQuery {
 
   import driver.api._
 
-  implicit val GetUUIDResult = GetResult(r => uuidColumnType.fromBytes(r.nextBytes()))
-  implicit val GetUUIDOptionResult = GetResult(r => Option(uuidColumnType.fromBytes(r.nextBytes())))
+  implicit val GetUUIDResult: GetResult[UUID] = GetResult(r => uuidColumnType.fromBytes(r.nextBytes()))
+  implicit val GetUUIDOptionResult: GetResult[Option[UUID]] =
+    GetResult(r => Option(uuidColumnType.fromBytes(r.nextBytes())))
   implicit object SetUUIDParameter extends SetParameter[UUID] {
     def apply(v: UUID, pp: PositionedParameters) { pp.setBytes(uuidColumnType.toBytes(v)) }
   }

core/src/main/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/EntityComponent.scala

@@ -237,7 +237,8 @@ trait EntityComponent {
     // noinspection SqlDialectInspection,DuplicatedCode
     private object EntityRecordRawSqlQuery extends RawSqlQuery {
       val driver: JdbcProfile = EntityComponent.this.driver
-      implicit val getEntityRecord = GetResult(r => EntityRecord(r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<))
+      implicit val getEntityRecord: GetResult[EntityRecord] =
+        GetResult(r => EntityRecord(r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<))
 
       def action(workspaceId: UUID, entities: Set[AttributeEntityReference]): ReadAction[Seq[EntityRecord]] =
         if (entities.isEmpty) {
@@ -317,7 +318,7 @@ trait EntityComponent {
       val driver: JdbcProfile = EntityComponent.this.driver
 
       // tells slick how to convert a result row from a raw sql query to an instance of EntityAndAttributesResult
-      implicit val getEntityAndAttributesResult = GetResult { r =>
+      implicit val getEntityAndAttributesResult: GetResult[EntityAndAttributesResult] = GetResult { r =>
         // note that the number and order of all the r.<< match precisely with the select clause of baseEntityAndAttributeSql
         val entityRec = EntityRecord(r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<)