[WX-1346] Scalafmt

.scalafmt.conf

@@ -0,0 +1,18 @@
+version = 3.7.17
+align.preset = none
+align.openParenCallSite = true
+align.openParenDefnSite = true
+maxColumn = 120
+continuationIndent.defnSite = 2
+assumeStandardLibraryStripMargin = true
+align.stripMargin = true
+danglingParentheses.preset = true
+rewrite.rules = [Imports, RedundantBraces, RedundantParens, SortModifiers]
+rewrite.imports.sort = scalastyle
+docstrings.style = keep
+project.excludeFilters = [
+  Dependencies.scala,
+  Settings.scala,
+  build.sbt
+]
+runner.dialect = scala213

CromIAM/src/main/scala/cromiam/auth/Collection.scala

@@ -9,6 +9,7 @@ import scala.util.{Success, Try}
 final case class Collection(name: String) extends AnyVal
 
 object Collection {
+
   /**
     * Parses a raw JSON string to make sure it fits the standard pattern (see below) for labels,
     * performs some CromIAM-specific checking to ensure the user isn't attempting to manipulate the
@@ -19,13 +20,14 @@ object Collection {
     */
   def validateLabels(labelsJson: Option[String]): Directive1[Option[Map[String, JsValue]]] = {
 
-      val labels = labelsJson map { l =>
-        Try(l.parseJson) match {
-          case Success(JsObject(json)) if json.keySet.contains(CollectionLabelName) => throw new LabelContainsCollectionException
-          case Success(JsObject(json)) => json
-          case _ => throw InvalidLabelsException(l)
-        }
+    val labels = labelsJson map { l =>
+      Try(l.parseJson) match {
+        case Success(JsObject(json)) if json.keySet.contains(CollectionLabelName) =>
+          throw new LabelContainsCollectionException
+        case Success(JsObject(json)) => json
+        case _ => throw InvalidLabelsException(l)
       }
+    }
 
     provide(labels)
   }
@@ -34,15 +36,16 @@ object Collection {
   val LabelsKey = "labels"
 
   // LabelContainsCollectionException is a class because of ScalaTest, some of the constructs don't play well w/ case objects
-  final class LabelContainsCollectionException extends Exception(s"Submitted labels contain the key $CollectionLabelName, which is not allowed\n")
-  final case class InvalidLabelsException(labels: String) extends Exception(s"Labels must be a valid JSON object, received: $labels\n")
+  final class LabelContainsCollectionException
+      extends Exception(s"Submitted labels contain the key $CollectionLabelName, which is not allowed\n")
+  final case class InvalidLabelsException(labels: String)
+      extends Exception(s"Labels must be a valid JSON object, received: $labels\n")
 
   /**
     * Returns the default collection for a user.
     */
-  def forUser(user: User): Collection = {
+  def forUser(user: User): Collection =
     Collection(user.userId.value)
-  }
 
   implicit val collectionJsonReader = new JsonReader[Collection] {
     import spray.json.DefaultJsonProtocol._

CromIAM/src/main/scala/cromiam/auth/User.scala

@@ -7,4 +7,3 @@ import org.broadinstitute.dsde.workbench.model.WorkbenchUserId
   * Wraps the concept of an authenticated workbench user including their numeric ID as well as their bearer token
   */
 final case class User(userId: WorkbenchUserId, authorization: Authorization)
-

CromIAM/src/main/scala/cromiam/cromwell/CromwellClient.scala

@@ -25,10 +25,16 @@ import scala.concurrent.{ExecutionContextExecutor, Future}
   *
   * FIXME: Look for ways to synch this up with the mothership
   */
-class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingAdapter, serviceRegistryActorRef: ActorRef)(implicit system: ActorSystem,
-                                                                                        ece: ExecutionContextExecutor,
-                                                                                        materializer: ActorMaterializer)
-  extends SprayJsonSupport with DefaultJsonProtocol with StatusCheckedSubsystem with CromIamInstrumentation{
+class CromwellClient(scheme: String,
+                     interface: String,
+                     port: Int,
+                     log: LoggingAdapter,
+                     serviceRegistryActorRef: ActorRef
+)(implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer)
+    extends SprayJsonSupport
+    with DefaultJsonProtocol
+    with StatusCheckedSubsystem
+    with CromIamInstrumentation {
 
   val cromwellUrl = new URL(s"$scheme://$interface:$port")
   val cromwellApiVersion = "v1"
@@ -41,35 +47,38 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
 
   def collectionForWorkflow(workflowId: String,
                             user: User,
-                            cromIamRequest: HttpRequest): FailureResponseOrT[Collection] = {
+                            cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Collection] = {
     import CromwellClient.EnhancedWorkflowLabels
 
     log.info("Requesting collection for " + workflowId + " for user " + user.userId + " from metadata")
 
     // Look up in Cromwell what the collection is for this workflow. If it doesn't exist, fail the Future
-    val cromwellApiLabelFunc = () => cromwellApiClient.labels(WorkflowId.fromString(workflowId), headers = List(user.authorization)) flatMap {
-      _.caasCollection match {
-        case Some(c) => FailureResponseOrT.pure[IO, HttpResponse](c)
-        case None =>
-          val exception = new IllegalArgumentException(s"Workflow $workflowId has no associated collection")
-          val failure = IO.raiseError[Collection](exception)
-          FailureResponseOrT.right[HttpResponse](failure)
+    val cromwellApiLabelFunc = () =>
+      cromwellApiClient.labels(WorkflowId.fromString(workflowId), headers = List(user.authorization)) flatMap {
+        _.caasCollection match {
+          case Some(c) => FailureResponseOrT.pure[IO, HttpResponse](c)
+          case None =>
+            val exception = new IllegalArgumentException(s"Workflow $workflowId has no associated collection")
+            val failure = IO.raiseError[Collection](exception)
+            FailureResponseOrT.right[HttpResponse](failure)
+        }
       }
-    }
 
     instrumentRequest(cromwellApiLabelFunc, cromIamRequest, wfCollectionPrefix)
   }
 
   def forwardToCromwell(httpRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
     val future = {
       // See CromwellClient's companion object for info on these header modifications
-      val headers = httpRequest.headers.filterNot(header => header.name == TimeoutAccessHeader || header.name == HostHeader)
+      val headers =
+        httpRequest.headers.filterNot(header => header.name == TimeoutAccessHeader || header.name == HostHeader)
       val cromwellRequest = httpRequest
         .copy(uri = httpRequest.uri.withAuthority(interface, port).withScheme(scheme))
         .withHeaders(headers)
       Http().singleRequest(cromwellRequest)
-    } recoverWith {
-      case e => Future.failed(CromwellConnectionFailure(e))
+    } recoverWith { case e =>
+      Future.failed(CromwellConnectionFailure(e))
     }
     future.asFailureResponseOrT
   }
@@ -86,7 +95,7 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
           use the current workflow id.
 
           This is all called from inside the context of a Future, so exceptions will be properly caught.
-      */
+       */
       metadata.value.parseJson.asJsObject.fields.get("rootWorkflowId").map(_.convertTo[String]).getOrElse(workflowId)
     }
 
@@ -96,11 +105,13 @@ class CromwellClient(scheme: String, interface: String, port: Int, log: LoggingA
       Grab the metadata from Cromwell filtered down to the rootWorkflowId. Then transform the response to get just the
       root workflow ID itself
      */
-    val cromwellApiMetadataFunc = () => cromwellApiClient.metadata(
-      WorkflowId.fromString(workflowId),
-      args = Option(Map("includeKey" -> List("rootWorkflowId"))),
-      headers = List(user.authorization)).map(metadataToRootWorkflowId
-    )
+    val cromwellApiMetadataFunc = () =>
+      cromwellApiClient
+        .metadata(WorkflowId.fromString(workflowId),
+                  args = Option(Map("includeKey" -> List("rootWorkflowId"))),
+                  headers = List(user.authorization)
+        )
+        .map(metadataToRootWorkflowId)
 
     instrumentRequest(cromwellApiMetadataFunc, cromIamRequest, rootWfIdPrefix)
   }
@@ -120,14 +131,14 @@ object CromwellClient {
   // See: https://broadworkbench.atlassian.net/browse/DDO-2190
   val HostHeader = "Host"
 
-  final case class CromwellConnectionFailure(f: Throwable) extends Exception(s"Unable to connect to Cromwell (${f.getMessage})", f)
+  final case class CromwellConnectionFailure(f: Throwable)
+      extends Exception(s"Unable to connect to Cromwell (${f.getMessage})", f)
 
   implicit class EnhancedWorkflowLabels(val wl: WorkflowLabels) extends AnyVal {
 
-    import Collection.{CollectionLabelName, collectionJsonReader}
+    import Collection.{collectionJsonReader, CollectionLabelName}
 
-    def caasCollection: Option[Collection] = {
+    def caasCollection: Option[Collection] =
       wl.labels.fields.get(CollectionLabelName).map(_.convertTo[Collection])
-    }
   }
 }

CromIAM/src/main/scala/cromiam/instrumentation/CromIamInstrumentation.scala

@@ -27,10 +27,11 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
   val rootWfIdPrefix = NonEmptyList.one("root-workflow-id")
   val wfCollectionPrefix = NonEmptyList.one("workflow-collection")
 
-
   def convertRequestToPath(httpRequest: HttpRequest): NonEmptyList[String] = NonEmptyList.of(
     // Returns the path of the URI only, without query parameters (e.g: api/engine/workflows/metadata)
-    httpRequest.uri.path.toString().stripPrefix("/")
+    httpRequest.uri.path
+      .toString()
+      .stripPrefix("/")
       // Replace UUIDs with [id] to keep paths same regardless of the workflow
       .replaceAll(CromIamInstrumentation.UUIDRegex, "[id]"),
     // Name of the method (e.g: GET)
@@ -43,15 +44,19 @@ trait CromIamInstrumentation extends CromwellInstrumentation {
   def makePathFromRequestAndResponse(httpRequest: HttpRequest, httpResponse: HttpResponse): InstrumentationPath =
     convertRequestToPath(httpRequest).concatNel(NonEmptyList.of(httpResponse.status.intValue.toString))
 
-  def sendTimingApi(statsDPath: InstrumentationPath, timing: FiniteDuration, prefixToStatsd: NonEmptyList[String]): Unit = {
+  def sendTimingApi(statsDPath: InstrumentationPath,
+                    timing: FiniteDuration,
+                    prefixToStatsd: NonEmptyList[String]
+  ): Unit =
     sendTiming(prefixToStatsd.concatNel(statsDPath), timing, CromIamPrefix)
-  }
 
-  def instrumentationPrefixForSam(methodPrefix: NonEmptyList[String]): NonEmptyList[String] = samPrefix.concatNel(methodPrefix)
+  def instrumentationPrefixForSam(methodPrefix: NonEmptyList[String]): NonEmptyList[String] =
+    samPrefix.concatNel(methodPrefix)
 
   def instrumentRequest[A](func: () => FailureResponseOrT[A],
                            httpRequest: HttpRequest,
-                           prefix: NonEmptyList[String]): FailureResponseOrT[A] = {
+                           prefix: NonEmptyList[String]
+  ): FailureResponseOrT[A] = {
     def now(): Deadline = Deadline.now
 
     val startTimestamp = now()

CromIAM/src/main/scala/cromiam/sam/SamClient.scala

@@ -33,20 +33,21 @@ class SamClient(scheme: String,
                 port: Int,
                 checkSubmitWhitelist: Boolean,
                 log: LoggingAdapter,
-                serviceRegistryActorRef: ActorRef)
-               (implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer) extends StatusCheckedSubsystem with CromIamInstrumentation {
+                serviceRegistryActorRef: ActorRef
+)(implicit system: ActorSystem, ece: ExecutionContextExecutor, materializer: ActorMaterializer)
+    extends StatusCheckedSubsystem
+    with CromIamInstrumentation {
 
-  private implicit val cs = IO.contextShift(ece)
+  implicit private val cs = IO.contextShift(ece)
 
   override val statusUri = uri"$samBaseUri/status"
   override val serviceRegistryActor: ActorRef = serviceRegistryActorRef
 
-  def isSubmitWhitelisted(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
+  def isSubmitWhitelisted(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] =
     checkSubmitWhitelist.fold(
       isSubmitWhitelistedSam(user, cromIamRequest),
       FailureResponseOrT.pure(true)
     )
-  }
 
   def isSubmitWhitelistedSam(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[Boolean] = {
     val request = HttpRequest(
@@ -64,7 +65,7 @@ class SamClient(scheme: String,
       whitelisted <- response.status match {
         case StatusCodes.OK =>
           // Does not seem to be already provided?
-          implicit val entityToBooleanUnmarshaller : Unmarshaller[HttpEntity, Boolean] =
+          implicit val entityToBooleanUnmarshaller: Unmarshaller[HttpEntity, Boolean] =
             (Unmarshaller.stringUnmarshaller flatMap Unmarshaller.booleanFromStringUnmarshaller).asScala
           val unmarshal = IO.fromFuture(IO(Unmarshal(response.entity).to[Boolean]))
           FailureResponseOrT.right[HttpResponse](unmarshal)
@@ -95,14 +96,19 @@ class SamClient(scheme: String,
             userInfo.enabled
           }
         case _ =>
-          log.error("Could not verify access with Sam for user {}, error was {} {}", user.userId, response.status, response.toString().take(100))
+          log.error("Could not verify access with Sam for user {}, error was {} {}",
+                    user.userId,
+                    response.status,
+                    response.toString().take(100)
+          )
           FailureResponseOrT.pure[IO, HttpResponse](false)
       }
     } yield userEnabled
   }
 
   def collectionsForUser(user: User, cromIamRequest: HttpRequest): FailureResponseOrT[List[Collection]] = {
-    val request = HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
+    val request =
+      HttpRequest(method = HttpMethods.GET, uri = samBaseCollectionUri, headers = List[HttpHeader](user.authorization))
 
     for {
       response <- instrumentRequest(
@@ -120,24 +126,25 @@ class SamClient(scheme: String,
     * @return Successful future if the auth is accepted, a Failure otherwise.
     */
   def requestAuth(authorizationRequest: CollectionAuthorizationRequest,
-                  cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
+                  cromIamRequest: HttpRequest
+  ): FailureResponseOrT[Unit] = {
     val logString = authorizationRequest.action + " access for user " + authorizationRequest.user.userId +
-      " on a request to " + authorizationRequest.action +  " for collection " + authorizationRequest.collection.name
+      " on a request to " + authorizationRequest.action + " for collection " + authorizationRequest.collection.name
 
-    def validateEntityBytes(byteString: ByteString): FailureResponseOrT[Unit] = {
+    def validateEntityBytes(byteString: ByteString): FailureResponseOrT[Unit] =
       if (byteString.utf8String == "true") {
         Monad[FailureResponseOrT].unit
       } else {
         log.warning("Sam denied " + logString)
         FailureResponseOrT[IO, HttpResponse, Unit](IO.raiseError(new SamDenialException))
       }
-    }
 
     log.info("Requesting authorization for " + logString)
 
     val request = HttpRequest(method = HttpMethods.GET,
-      uri = samAuthorizeActionUri(authorizationRequest),
-      headers = List[HttpHeader](authorizationRequest.user.authorization))
+                              uri = samAuthorizeActionUri(authorizationRequest),
+                              headers = List[HttpHeader](authorizationRequest.user.authorization)
+    )
 
     for {
       response <- instrumentRequest(
@@ -158,26 +165,28 @@ class SamClient(scheme: String,
             - If user has the 'add' permission we're ok
         - else fail the future
    */
-  def requestSubmission(user: User,
-                        collection: Collection,
-                        cromIamRequest: HttpRequest
-                       ): FailureResponseOrT[Unit] = {
+  def requestSubmission(user: User, collection: Collection, cromIamRequest: HttpRequest): FailureResponseOrT[Unit] = {
     log.info("Verifying user " + user.userId + " can submit a workflow to collection " + collection.name)
     val createCollection = registerCreation(user, collection, cromIamRequest)
 
     createCollection flatMap {
       case r if r.status == StatusCodes.NoContent => Monad[FailureResponseOrT].unit
       case r => FailureResponseOrT[IO, HttpResponse, Unit](IO.raiseError(SamRegisterCollectionException(r.status)))
     } recoverWith {
-      case r if r.status == StatusCodes.Conflict => requestAuth(CollectionAuthorizationRequest(user, collection, "add"), cromIamRequest)
+      case r if r.status == StatusCodes.Conflict =>
+        requestAuth(CollectionAuthorizationRequest(user, collection, "add"), cromIamRequest)
       case r => FailureResponseOrT[IO, HttpResponse, Unit](IO.raiseError(SamRegisterCollectionException(r.status)))
     }
   }
 
   protected def registerCreation(user: User,
                                  collection: Collection,
-                                 cromIamRequest: HttpRequest): FailureResponseOrT[HttpResponse] = {
-    val request = HttpRequest(method = HttpMethods.POST, uri = samRegisterUri(collection), headers = List[HttpHeader](user.authorization))
+                                 cromIamRequest: HttpRequest
+  ): FailureResponseOrT[HttpResponse] = {
+    val request = HttpRequest(method = HttpMethods.POST,
+                              uri = samRegisterUri(collection),
+                              headers = List[HttpHeader](user.authorization)
+    )
 
     instrumentRequest(
       () => Http().singleRequest(request).asFailureResponseOrT,
@@ -186,9 +195,9 @@ class SamClient(scheme: String,
     )
   }
 
-  private def samAuthorizeActionUri(authorizationRequest: CollectionAuthorizationRequest) = {
-    akka.http.scaladsl.model.Uri(s"${samBaseUriForWorkflow(authorizationRequest.collection)}/action/${authorizationRequest.action}")
-  }
+  private def samAuthorizeActionUri(authorizationRequest: CollectionAuthorizationRequest) =
+    akka.http.scaladsl.model
+      .Uri(s"${samBaseUriForWorkflow(authorizationRequest.collection)}/action/${authorizationRequest.action}")
 
   private def samRegisterUri(collection: Collection) = akka.http.scaladsl.model.Uri(samBaseUriForWorkflow(collection))
 
@@ -207,15 +216,18 @@ object SamClient {
 
   class SamDenialException extends Exception("Access Denied")
 
-  final case class SamConnectionFailure(phase: String, f: Throwable) extends Exception(s"Unable to connect to Sam during $phase (${f.getMessage})", f)
+  final case class SamConnectionFailure(phase: String, f: Throwable)
+      extends Exception(s"Unable to connect to Sam during $phase (${f.getMessage})", f)
 
-  final case class SamRegisterCollectionException(errorCode: StatusCode) extends Exception(s"Can't register collection with Sam. Status code: ${errorCode.value}")
+  final case class SamRegisterCollectionException(errorCode: StatusCode)
+      extends Exception(s"Can't register collection with Sam. Status code: ${errorCode.value}")
 
   final case class CollectionAuthorizationRequest(user: User, collection: Collection, action: String)
 
   val SamDenialResponse = HttpResponse(status = StatusCodes.Forbidden, entity = new SamDenialException().getMessage)
 
-  def SamRegisterCollectionExceptionResp(statusCode: StatusCode) = HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
+  def SamRegisterCollectionExceptionResp(statusCode: StatusCode) =
+    HttpResponse(status = statusCode, entity = SamRegisterCollectionException(statusCode).getMessage)
 
   case class UserStatusInfo(adminEnabled: Boolean, enabled: Boolean, userEmail: String, userSubjectId: String)