WX-772 Update Scala to 2.13.9

CHANGELOG.md

@@ -32,6 +32,11 @@ supported.
 All DRS inputs to a task are now localized in a single PAPI action, which should improve speed and resolve
 failures observed when attempting to localize a large number of DRS files.
 
+### Security Patching
+
+Updates to dependencies to fix security vulnerabilities.
+
+
 ## 84 Release Notes
 
 ### CromIAM enabled user checks

backend/src/main/scala/cromwell/backend/standard/StandardCachingActorHelper.scala

@@ -78,7 +78,7 @@ trait StandardCachingActorHelper extends JobCachingActorHelper {
 
     val fileMetadata = jobPaths.metadataPaths
 
-    runtimeAttributesMetadata ++ fileMetadata ++ nonStandardMetadata
+    nonStandardMetadata ++ runtimeAttributesMetadata ++ fileMetadata
   }
 
   /**

backend/src/main/scala/cromwell/backend/standard/callcaching/RootWorkflowFileHashCacheActor.scala

@@ -48,7 +48,7 @@ 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[Any, Any](hashCommand.fileHashContext, IoSuccess(requester.ioCommand, value))
         case FileHashFailure(error) =>
           sender() ! Tuple2(hashCommand.fileHashContext, IoFailure(requester.ioCommand, new IOException(error)))
       }

centaur/src/it/scala/centaur/reporting/BigQueryReporter.scala

@@ -189,7 +189,7 @@ class BigQueryReporter(override val params: ErrorReporterParams) extends ErrorRe
   }
 
   private def toJobKeyValueRow(jobKeyValueEntry: JobKeyValueEntry): RowToInsert = {
-    RowToInsert of Map(
+    RowToInsert of Map[String, Any](
       "call_fully_qualified_name" -> jobKeyValueEntry.callFullyQualifiedName,
       "job_attempt" -> jobKeyValueEntry.jobAttempt,
       "job_index" -> jobKeyValueEntry.jobIndex,

codegen_java/build.sbt

@@ -6,7 +6,7 @@ lazy val root = (project in file(".")).
     Seq(organization := "org.broadinstitute.cromwell",
     name := "cromwell-client",
     version := createVersion("0.1"),
-    scalaVersion := "2.13.8",
+    scalaVersion := "2.13.9",
     scalacOptions ++= Seq("-feature"),
     compile / javacOptions ++= Seq("-Xlint:deprecation"),
     Compile / packageDoc / publishArtifact := false,

common/src/main/scala/common/util/TerminalUtil.scala

@@ -6,10 +6,10 @@ object TerminalUtil {
     def maxWidth(lengths: Seq[Seq[Int]], column: Int) = lengths.map { length => length(column) }.max
     val widths = (rows :+ header).map { row => row.map { s => s.length } }
     val maxWidths = widths.head.indices.map { column => maxWidth(widths, column) }
-    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+    val tableHeader = header.indices.map { i => header(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
     val tableDivider = header.indices.map { i => "-" * maxWidths(i) }.mkString("|")
     val tableRows = rows.map { row =>
-      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), " ").mkString("") }.mkString("|")
+      val mdRow = row.indices.map { i => row(i).padTo(maxWidths(i), ' ').mkString("") }.mkString("|")
       s"|$mdRow|"
     }
     s"|$tableHeader|\n|$tableDivider|\n${tableRows.mkString("\n")}\n"

common/src/test/scala/common/collections/EnhancedCollectionsSpec.scala

@@ -11,7 +11,7 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   behavior of "EnhancedCollections"
 
   it should "filter a List by type and return a List" in {
-    val objectList = List("hello", 3, None, "world")
+    val objectList = List[Any]("hello", 3, None, "world")
     val stringList = objectList.filterByType[String]
 
     stringList should be(List("hello", "world"))
@@ -28,14 +28,14 @@ class EnhancedCollectionsSpec extends AsyncFlatSpec with Matchers {
   }
 
   it should "filter a Set by type and return a Set" in {
-    val objectSet = Set("hello", 3, None, "world")
+    val objectSet = Set[Any]("hello", 3, None, "world")
     val intSet: Set[Int] = objectSet.filterByType[Int]
 
     intSet should be(Set(3))
   }
 
   it should "find the first Int in a List" in {
-    val objectSet = List("hello", 3, None, 4, "world")
+    val objectSet = List[Any]("hello", 3, None, 4, "world")
     objectSet.firstByType[Int] should be(Some(3))
   }
 

core/src/test/scala/cromwell/core/io/IoClientHelperSpec.scala

@@ -27,7 +27,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
     val testActor = TestActorRef(new IoClientHelperTestActor(ioActorProbe.ref, delegateProbe.ref, backoff, noResponseTimeout))
 
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessage(command)
@@ -58,7 +58,7 @@ class IoClientHelperSpec extends TestKitSuite with AnyFlatSpecLike with Matchers
 
     val commandContext = "context"
     val command = DefaultIoSizeCommand(mock[Path])
-    val response = IoSuccess(command, 5)
+    val response = IoSuccess(command, 5L)
 
     // Send the command
     testActor.underlyingActor.sendMessageWithContext(commandContext, command)

core/src/test/scala/cromwell/core/retry/BackoffSpec.scala

@@ -54,7 +54,7 @@ class BackoffSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
 
   it should "parse config" in {
     val config = ConfigFactory.parseMap(
-      Map(
+      Map[String, Any](
         "min" -> "5 seconds",
         "max" -> "30 seconds",
         "multiplier" -> 6D,

engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/callcaching/FetchCachedResultsActor.scala

@@ -37,7 +37,7 @@ class FetchCachedResultsActor(cacheResultId: CallCachingEntryId, replyTo: ActorR
 
         val sourceCacheDetails = Seq(result.callCachingEntry.workflowExecutionUuid,
           result.callCachingEntry.callFullyQualifiedName,
-          result.callCachingEntry.jobIndex).mkString(":")
+          result.callCachingEntry.jobIndex.toString).mkString(":")
 
         CachedOutputLookupSucceeded(simpletons, jobDetritusFiles.toMap,
           result.callCachingEntry.returnCode,

engine/src/main/scala/cromwell/engine/workflow/lifecycle/execution/job/EngineJobExecutionActor.scala

@@ -753,7 +753,7 @@ class EngineJobExecutionActor(replyTo: ActorRef,
 
   private def logCacheHitSuccessAndNotifyMetadata(data: ResponsePendingData): Unit = {
 
-    val metadataMap = Map(callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
+    val metadataMap = Map[String, Any](callCachingHitResultMetadataKey -> true) ++ data.ejeaCacheHit.flatMap(_.details).map(details => callCachingReadResultMetadataKey -> s"Cache Hit: $details").toMap
 
     writeToMetadata(metadataMap)
 

engine/src/test/scala/cromwell/engine/workflow/lifecycle/ValidatingCachingConfigSpec.scala

@@ -11,7 +11,7 @@ import scala.util.{Failure, Success, Try}
 class ValidatingCachingConfigSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers with TableDrivenPropertyChecks {
 
     it should "run config tests" in {
-      val cases = Table(
+      val cases = Table[String, Any](
         ("config"                 , "exceptionMessage"                                                              ),
         ("enabled = not-a-boolean", "String: 1: enabled has type STRING rather than BOOLEAN"                        ),
         ("enabled = true"         , true                                                                            ),

project/Dependencies.scala

@@ -89,7 +89,7 @@ object Dependencies {
   private val postgresV = "42.3.3"
   private val pprintV = "0.7.3"
   private val rdf4jV = "3.7.1"
-  private val refinedV = "0.9.29"
+  private val refinedV = "0.10.1"
   private val rhinoV = "1.7.14"
 
   private val scalaCollectionCompatV = "2.5.0"
@@ -480,7 +480,8 @@ object Dependencies {
   val coreDependencies: List[ModuleID] = List(
     "com.google.auth" % "google-auth-library-oauth2-http" % googleOauth2V,
     "com.chuusai" %% "shapeless" % shapelessV,
-    "com.storm-enroute" %% "scalameter" % scalameterV % Test,
+    "com.storm-enroute" %% "scalameter" % scalameterV % Test
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.github.scopt" %% "scopt" % scoptV,
   ) ++ akkaStreamDependencies ++ configDependencies ++ catsDependencies ++ circeDependencies ++
     googleApiClientDependencies ++ statsDDependencies ++ betterFilesDependencies ++
@@ -509,7 +510,8 @@ object Dependencies {
     "com.storm-enroute" %% "scalameter" % scalameterV
       exclude("com.fasterxml.jackson.core", "jackson-databind")
       exclude("com.fasterxml.jackson.module", "jackson-module-scala")
-      exclude("org.scala-tools.testing", "test-interface"),
+      exclude("org.scala-tools.testing", "test-interface")
+      exclude("org.scala-lang.modules", "scala-xml_2.13"),
     "com.fasterxml.jackson.core" % "jackson-databind" % jacksonV,
     "io.github.andrebeat" %% "scala-pool" % scalaPoolV
   ) ++ swaggerUiDependencies ++ akkaHttpDependencies ++ akkaHttpCirceIntegrationDependency ++ circeDependencies ++

project/Settings.scala

@@ -70,7 +70,7 @@ object Settings {
     assembly / assemblyMergeStrategy := customMergeStrategy.value,
   )
 
-  val Scala2_13Version = "2.13.8"
+  val Scala2_13Version = "2.13.9"
   private val ScalaVersion: String = Scala2_13Version
   private val sharedSettings: Seq[Setting[_]] =
     cromwellVersionWithGit ++ publishingSettings ++ List(

project/plugins.sbt

@@ -1,5 +1,5 @@
 addSbtPlugin("se.marcuslonnberg" % "sbt-docker" % "1.9.0")
 addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.1")
 addSbtPlugin("com.github.sbt" % "sbt-git" % "2.0.0")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.9.3")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.0.4")
 addDependencyTreePlugin

services/src/main/scala/cromwell/services/instrumentation/impl/selectivetsv/SelectiveTsvInstrumentationServiceActor.scala

@@ -143,7 +143,7 @@ object SelectiveTsvInstrumentationServiceActor {
 
       val header = (List("timestamp") ++ interestingFields).mkString("\t")
       val rows = stateHistory.map { case (timestamp, fieldMap) =>
-        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0))).mkString("\t")
+        (Vector(timestamp.toString) ++ interestingFields.map(f => fieldMap.getOrElse(f, 0).toString)).mkString("\t")
       }
       Vector(header) ++ rows
     }

services/src/test/scala/cromwell/services/metadata/impl/MetadataDatabaseAccessSpec.scala

@@ -287,7 +287,7 @@ class MetadataDatabaseAccessSpec extends AnyFlatSpec with CromwellTimeoutSpec wi
         }
         // Filter by workflow id within random Ids
         _ <- dataAccess.queryWorkflowSummaries(WorkflowQueryParameters(
-          (randomIds :+ workflow1Id).map(id => WorkflowQueryKey.Id.name -> id.toString))) map { case (response, _) =>
+          (randomIds :+ workflow1Id.toString).map(id => WorkflowQueryKey.Id.name -> id))) map { case (response, _) =>
           val resultsById = response.results groupBy {
             _.name
           }

supportedBackends/google/pipelines/common/src/main/scala/cromwell/backend/google/pipelines/common/PipelinesApiJobCachingActorHelper.scala

@@ -75,7 +75,7 @@ trait PipelinesApiJobCachingActorHelper extends StandardCachingActorHelper {
       .get(WorkflowOptionKeys.GoogleProject)
       .getOrElse(jesAttributes.project)
 
-    Map(
+    Map[String, Any](
       PipelinesApiMetadataKeys.GoogleProject -> googleProject,
       PipelinesApiMetadataKeys.ExecutionBucket -> initializationData.workflowPaths.executionRootString,
       PipelinesApiMetadataKeys.EndpointUrl -> jesAttributes.endpointUrl,

supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/PipelinesApiAsyncBackendJobExecutionActor.scala

@@ -141,9 +141,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(

supportedBackends/google/pipelines/v2alpha1/src/test/scala/cromwell/backend/google/pipelines/v2alpha1/api/DeserializationSpec.scala

@@ -82,9 +82,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -117,7 +117,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",

supportedBackends/google/pipelines/v2beta/src/main/scala/cromwell/backend/google/pipelines/v2beta/PipelinesApiAsyncBackendJobExecutionActor.scala

@@ -146,9 +146,9 @@ class PipelinesApiAsyncBackendJobExecutionActor(standardParams: StandardAsyncExe
       }
 
       val optional = Option(output) collectFirst { case o: PipelinesApiFileOutput if o.secondary || o.optional => "optional" } getOrElse "required"
-      val contentType = output.contentType.getOrElse("")
+      val contentType = output.contentType.map(_.toString).getOrElse("")
 
-      List(kind, output.cloudPath, output.containerPath, optional, contentType)
+      List(kind, output.cloudPath.toString, output.containerPath.toString, optional, contentType)
     } mkString("\"", "\"\n|  \"", "\"")
 
     val parallelCompositeUploadThreshold = jobDescriptor.workflowDescriptor.workflowOptions.getOrElse(

supportedBackends/google/pipelines/v2beta/src/test/scala/cromwell/backend/google/pipelines/v2beta/api/DeserializationSpec.scala

@@ -81,9 +81,9 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
-          "virtualMachine" -> Map(
+          "virtualMachine" -> Map[String, Any](
             "machineType" -> "custom-1-1024",
             "preemptible" -> false
           ).asJava
@@ -115,7 +115,7 @@ class DeserializationSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matc
             "commands" -> List[String]("echo", "hello").asJava
           ).asJava
         ).asJava,
-        "resources" -> Map(
+        "resources" -> Map[String, Object](
           "projectId" -> "project",
           "virtualMachine" -> Map(
             "machineType" -> "custom-1-1024",

wdl/model/draft2/src/main/scala/wdl/draft2/model/AstTools.scala

@@ -196,7 +196,7 @@ object AstTools {
           val pairType = womType.asInstanceOf[WomPairType]
           WomPair(subElements.head.womValue(pairType.leftType, wdlSyntaxErrorFormatter), subElements(1).womValue(pairType.rightType, wdlSyntaxErrorFormatter))
         } else {
-          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+          throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
         }
       }
 
@@ -224,7 +224,7 @@ object AstTools {
         case a: Ast if a.getName == "TupleLiteral" => astTupleToValue(a)
         case a: Ast if a.getName == "MapLiteral" && womType.isInstanceOf[WomMapType] => astToMap(a)
         case a: Ast if a.getName == "ObjectLiteral" && womType == WomObjectType => astToObject(a)
-        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).getOrElse("No AST").toString})")
+        case _ => throw new SyntaxError(s"Could not convert AST to a $womType (${Option(astNode).map(_.toString).getOrElse("No AST")})")
       }
     }
   }

wom/src/test/scala/wom/types/WomFileTypeSpec.scala

@@ -65,7 +65,7 @@ class WomFileTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers
     }
   }
 
-  lazy val failedCoercionTests = Table(
+  lazy val failedCoercionTests = Table[String, WomType, Any, String](
     ("description", "womFileType", "value", "expected"),
 
     ("a double to a dir", WomUnlistedDirectoryType, 6.28318,

wom/src/test/scala/wom/types/WomTypeSpec.scala

@@ -10,6 +10,7 @@ import wom.values._
 
 import scala.runtime.ScalaRunTime
 import scala.util.Random
+import scala.util.matching.Regex
 
 
 class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
@@ -32,7 +33,7 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
     WomSingleFileType.stableName shouldEqual "File"
   }
 
-  val rawValuesCoercedToType = Table(
+  val rawValuesCoercedToType = Table[Any, WomType, Any, Regex](
     (
       "Raw Value",
       "WomType",
@@ -43,33 +44,33 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       WomString("hello"),
       WomIntegerType,
       classOf[NumberFormatException],
-      "For input string: \"hello\""
+      "For input string: \"hello\"".r
     ),
     (
       WomInteger(0),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'."""
+      """No coercion defined from wom value\(s\) '0' of type 'Int' to 'Boolean'.""".r
     ),
     (
       0,
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'."
+      "No coercion defined from '0' of type 'java.lang.Integer' to 'Boolean'.".r
     ),
     (
       Array(0, 1, 2, 3, 4),
       WomBooleanType,
       classOf[IllegalArgumentException],
-      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'."""
+      """No coercion defined from 'Array\(0, 1, 2\)' of type 'int\[\]' to 'Boolean'.""".r
     ),
     (
       new AnyRef {},
       WomBooleanType,
       classOf[IllegalArgumentException],
-      "No coercion defined from" +
+      ("No coercion defined from" +
         """ 'wom.types.WomTypeSpec\$\$anon\$(.*)@.*' of type""" +
-        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'."""
+        """ 'wom.types.WomTypeSpec\$\$anon\$\1' to 'Boolean'.""").r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(
@@ -81,19 +82,19 @@ class WomTypeSpec extends AnyFlatSpec with CromwellTimeoutSpec with Matchers {
       ),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[0, 1, 2\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomArray(WomArrayType(WomOptionalType(WomIntegerType)), Seq(WomOptionalValue.none(WomIntegerType))),
       WomOptionalType(WomMaybeEmptyArrayType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'."""
+      """No coercion defined from wom value\(s\) '\[null\]' of type 'Array\[Int\?\]' to 'Array\[Int\]\?'.""".r
     ),
     (
       WomOptionalValue.none(WomArrayType(WomIntegerType)),
       WomMaybeEmptyArrayType(WomOptionalType(WomIntegerType)),
       classOf[IllegalArgumentException],
-      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'."""
+      """No coercion defined from wom value\(s\) 'null' of type 'Array\[Int\]\?' to 'Array\[Int\?\]'.""".r
     )
   )