Apply auto-formatting rules

wellcomecollection · May 22, 2019 · 2d4ab66 · 2d4ab66
1 parent cc145d2
commit 2d4ab66
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diff --git a/bag_auditor/src/main/scala/uk/ac/wellcome/platform/storage/bagauditor/Main.scala b/bag_auditor/src/main/scala/uk/ac/wellcome/platform/storage/bagauditor/Main.scala
@@ -5,13 +5,32 @@ import akka.stream.ActorMaterializer
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.sqs.AmazonSQSAsync
 import com.typesafe.config.Config
-import uk.ac.wellcome.messaging.typesafe.{AlpakkaSqsWorkerConfigBuilder, CloudwatchMonitoringClientBuilder, SQSBuilder}
+import uk.ac.wellcome.messaging.typesafe.{
+  AlpakkaSqsWorkerConfigBuilder,
+  CloudwatchMonitoringClientBuilder,
+  SQSBuilder
+}
 import uk.ac.wellcome.messaging.worker.monitoring.CloudwatchMonitoringClient
-import uk.ac.wellcome.platform.archive.common.config.builders.{IngestUpdaterBuilder, OperationNameBuilder, OutgoingPublisherBuilder}
-import uk.ac.wellcome.platform.archive.common.versioning.{DynamoIngestVersionManagerDao, IngestVersionManager, IngestVersionManagerDao}
-import uk.ac.wellcome.platform.storage.bagauditor.services.{BagAuditor, BagAuditorWorker}
+import uk.ac.wellcome.platform.archive.common.config.builders.{
+  IngestUpdaterBuilder,
+  OperationNameBuilder,
+  OutgoingPublisherBuilder
+}
+import uk.ac.wellcome.platform.archive.common.versioning.{
+  DynamoIngestVersionManagerDao,
+  IngestVersionManager,
+  IngestVersionManagerDao
+}
+import uk.ac.wellcome.platform.storage.bagauditor.services.{
+  BagAuditor,
+  BagAuditorWorker
+}
 import uk.ac.wellcome.platform.storage.bagauditor.versioning.VersionPicker
-import uk.ac.wellcome.storage.typesafe.{DynamoBuilder, LockingBuilder, S3Builder}
+import uk.ac.wellcome.storage.typesafe.{
+  DynamoBuilder,
+  LockingBuilder,
+  S3Builder
+}
 import uk.ac.wellcome.typesafe.WellcomeTypesafeApp
 import uk.ac.wellcome.typesafe.config.builders.AkkaBuilder
 

diff --git a/...ditor/src/main/scala/uk/ac/wellcome/platform/storage/bagauditor/services/BagAuditor.scala b/...ditor/src/main/scala/uk/ac/wellcome/platform/storage/bagauditor/services/BagAuditor.scala
@@ -3,10 +3,18 @@ package uk.ac.wellcome.platform.storage.bagauditor.services
 import java.time.Instant
 
 import com.amazonaws.services.s3.AmazonS3
-import uk.ac.wellcome.platform.archive.common.bagit.models.{BagInfo, ExternalIdentifier}
+import uk.ac.wellcome.platform.archive.common.bagit.models.{
+  BagInfo,
+  ExternalIdentifier
+}
 import uk.ac.wellcome.platform.archive.common.IngestID
 import uk.ac.wellcome.platform.archive.common.storage.StreamUnavailable
-import uk.ac.wellcome.platform.archive.common.storage.models.{IngestFailed, IngestStepResult, IngestStepSucceeded, StorageSpace}
+import uk.ac.wellcome.platform.archive.common.storage.models.{
+  IngestFailed,
+  IngestStepResult,
+  IngestStepSucceeded,
+  StorageSpace
+}
 import uk.ac.wellcome.platform.storage.bagauditor.models._
 import uk.ac.wellcome.platform.archive.common.storage.services.S3BagLocator
 import uk.ac.wellcome.platform.archive.common.storage.services.S3StreamableInstances._
@@ -82,8 +90,8 @@ class BagAuditor(versionPicker: VersionPicker)(implicit s3Client: AmazonS3) {
     for {
       bagInfoLocation <- s3BagLocator.locateBagInfo(bagRootLocation)
       inputStream <- bagInfoLocation.toInputStream match {
-        case Left(e) => Failure(e)
-        case Right(None) => Failure(StreamUnavailable("No stream available!"))
+        case Left(e)                  => Failure(e)
+        case Right(None)              => Failure(StreamUnavailable("No stream available!"))
         case Right(Some(inputStream)) => Success(inputStream)
       }
       bagInfo <- BagInfo.create(inputStream)

diff --git a/bag_register/src/main/scala/uk/ac/wellcome/platform/archive/bag_register/Main.scala b/bag_register/src/main/scala/uk/ac/wellcome/platform/archive/bag_register/Main.scala
@@ -6,20 +6,33 @@ import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.sqs.AmazonSQSAsync
 import com.typesafe.config.Config
 import uk.ac.wellcome.json.JsonUtil._
-import uk.ac.wellcome.messaging.typesafe.{AlpakkaSqsWorkerConfigBuilder, CloudwatchMonitoringClientBuilder, SQSBuilder}
+import uk.ac.wellcome.messaging.typesafe.{
+  AlpakkaSqsWorkerConfigBuilder,
+  CloudwatchMonitoringClientBuilder,
+  SQSBuilder
+}
 import uk.ac.wellcome.messaging.worker.monitoring.CloudwatchMonitoringClient
-import uk.ac.wellcome.platform.archive.bag_register.services.{BagRegisterWorker, Register}
-import uk.ac.wellcome.platform.archive.common.config.builders.{IngestUpdaterBuilder, OperationNameBuilder, OutgoingPublisherBuilder}
+import uk.ac.wellcome.platform.archive.bag_register.services.{
+  BagRegisterWorker,
+  Register
+}
+import uk.ac.wellcome.platform.archive.common.config.builders.{
+  IngestUpdaterBuilder,
+  OperationNameBuilder,
+  OutgoingPublisherBuilder
+}
 import uk.ac.wellcome.platform.archive.common.storage.models.StorageManifest
-import uk.ac.wellcome.platform.archive.common.storage.services.{StorageManifestService, StorageManifestVHS}
+import uk.ac.wellcome.platform.archive.common.storage.services.{
+  StorageManifestService,
+  StorageManifestVHS
+}
 import uk.ac.wellcome.storage.typesafe.{S3Builder, VHSBuilder}
 import uk.ac.wellcome.storage.vhs.EmptyMetadata
 import uk.ac.wellcome.typesafe.WellcomeTypesafeApp
 import uk.ac.wellcome.typesafe.config.builders.AkkaBuilder
 
 import scala.concurrent.ExecutionContext
 
-
 object Main extends WellcomeTypesafeApp {
   runWithConfig { config: Config =>
     implicit val actorSystem: ActorSystem =

diff --git a/bag_replicator/src/main/scala/uk/ac/wellcome/platform/archive/bagreplicator/Main.scala b/bag_replicator/src/main/scala/uk/ac/wellcome/platform/archive/bagreplicator/Main.scala
@@ -5,13 +5,24 @@ import akka.stream.ActorMaterializer
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.sqs.AmazonSQSAsync
 import com.typesafe.config.Config
-import uk.ac.wellcome.messaging.typesafe.{AlpakkaSqsWorkerConfigBuilder, CloudwatchMonitoringClientBuilder, SQSBuilder}
+import uk.ac.wellcome.messaging.typesafe.{
+  AlpakkaSqsWorkerConfigBuilder,
+  CloudwatchMonitoringClientBuilder,
+  SQSBuilder
+}
 import uk.ac.wellcome.messaging.worker.models.Result
 import uk.ac.wellcome.messaging.worker.monitoring.CloudwatchMonitoringClient
 import uk.ac.wellcome.platform.archive.bagreplicator.config.ReplicatorDestinationConfig
 import uk.ac.wellcome.platform.archive.bagreplicator.models.ReplicationSummary
-import uk.ac.wellcome.platform.archive.bagreplicator.services.{BagReplicator, BagReplicatorWorker}
-import uk.ac.wellcome.platform.archive.common.config.builders.{IngestUpdaterBuilder, OperationNameBuilder, OutgoingPublisherBuilder}
+import uk.ac.wellcome.platform.archive.bagreplicator.services.{
+  BagReplicator,
+  BagReplicatorWorker
+}
+import uk.ac.wellcome.platform.archive.common.config.builders.{
+  IngestUpdaterBuilder,
+  OperationNameBuilder,
+  OutgoingPublisherBuilder
+}
 import uk.ac.wellcome.storage.typesafe.{LockingBuilder, S3Builder}
 import uk.ac.wellcome.typesafe.WellcomeTypesafeApp
 import uk.ac.wellcome.typesafe.config.builders.AkkaBuilder

diff --git a/...in/scala/uk/ac/wellcome/platform/archive/bagreplicator/services/BagReplicatorWorker.scala b/...in/scala/uk/ac/wellcome/platform/archive/bagreplicator/services/BagReplicatorWorker.scala
@@ -8,7 +8,10 @@ import com.amazonaws.services.sqs.AmazonSQSAsync
 import com.amazonaws.services.sqs.model.{Message => SQSMessage}
 import grizzled.slf4j.Logging
 import uk.ac.wellcome.json.JsonUtil._
-import uk.ac.wellcome.messaging.sqsworker.alpakka.{AlpakkaSQSWorker, AlpakkaSQSWorkerConfig}
+import uk.ac.wellcome.messaging.sqsworker.alpakka.{
+  AlpakkaSQSWorker,
+  AlpakkaSQSWorkerConfig
+}
 import uk.ac.wellcome.messaging.worker.models.{NonDeterministicFailure, Result}
 import uk.ac.wellcome.messaging.worker.monitoring.MonitoringClient
 import uk.ac.wellcome.platform.archive.bagreplicator.config.ReplicatorDestinationConfig
@@ -21,7 +24,6 @@ import uk.ac.wellcome.storage.{LockDao, LockingService, ObjectLocation}
 import uk.ac.wellcome.typesafe.Runnable
 import cats.instances.future._
 
-
 import scala.concurrent.{ExecutionContext, Future}
 
 class BagReplicatorWorker(

diff --git a/bag_verifier/src/main/scala/uk/ac/wellcome/platform/archive/bagverifier/Main.scala b/bag_verifier/src/main/scala/uk/ac/wellcome/platform/archive/bagverifier/Main.scala
@@ -5,12 +5,26 @@ import akka.stream.ActorMaterializer
 import com.amazonaws.services.s3.AmazonS3
 import com.amazonaws.services.sqs.AmazonSQSAsync
 import com.typesafe.config.Config
-import uk.ac.wellcome.messaging.typesafe.{AlpakkaSqsWorkerConfigBuilder, CloudwatchMonitoringClientBuilder, SQSBuilder}
+import uk.ac.wellcome.messaging.typesafe.{
+  AlpakkaSqsWorkerConfigBuilder,
+  CloudwatchMonitoringClientBuilder,
+  SQSBuilder
+}
 import uk.ac.wellcome.messaging.worker.monitoring.MonitoringClient
-import uk.ac.wellcome.platform.archive.bagverifier.services.{BagVerifier, BagVerifierWorker}
+import uk.ac.wellcome.platform.archive.bagverifier.services.{
+  BagVerifier,
+  BagVerifierWorker
+}
 import uk.ac.wellcome.platform.archive.common.bagit.services.BagService
-import uk.ac.wellcome.platform.archive.common.config.builders.{IngestUpdaterBuilder, OperationNameBuilder, OutgoingPublisherBuilder}
-import uk.ac.wellcome.platform.archive.common.storage.services.{S3ObjectVerifier, S3Resolvable}
+import uk.ac.wellcome.platform.archive.common.config.builders.{
+  IngestUpdaterBuilder,
+  OperationNameBuilder,
+  OutgoingPublisherBuilder
+}
+import uk.ac.wellcome.platform.archive.common.storage.services.{
+  S3ObjectVerifier,
+  S3Resolvable
+}
 import uk.ac.wellcome.storage.typesafe.S3Builder
 import uk.ac.wellcome.typesafe.WellcomeTypesafeApp
 import uk.ac.wellcome.typesafe.config.builders.AkkaBuilder

diff --git a/...c/main/scala/uk/ac/wellcome/platform/archive/bagverifier/models/VerificationSummary.scala b/...c/main/scala/uk/ac/wellcome/platform/archive/bagverifier/models/VerificationSummary.scala
@@ -3,7 +3,12 @@ package uk.ac.wellcome.platform.archive.bagverifier.models
 import java.time.Instant
 
 import uk.ac.wellcome.platform.archive.common.operation.models.Summary
-import uk.ac.wellcome.platform.archive.common.verify.{VerificationFailure, VerificationIncomplete, VerificationResult, VerificationSuccess}
+import uk.ac.wellcome.platform.archive.common.verify.{
+  VerificationFailure,
+  VerificationIncomplete,
+  VerificationResult,
+  VerificationSuccess
+}
 import uk.ac.wellcome.storage.ObjectLocation
 
 sealed trait VerificationSummary extends Summary {

diff --git a/...ier/src/main/scala/uk/ac/wellcome/platform/archive/bagverifier/services/BagVerifier.scala b/...ier/src/main/scala/uk/ac/wellcome/platform/archive/bagverifier/services/BagVerifier.scala
@@ -5,7 +5,10 @@ import java.time.Instant
 import grizzled.slf4j.Logging
 import uk.ac.wellcome.platform.archive.bagverifier.models._
 import uk.ac.wellcome.platform.archive.common.bagit.models._
-import uk.ac.wellcome.platform.archive.common.bagit.services.{BagService, BagVerifiable}
+import uk.ac.wellcome.platform.archive.common.bagit.services.{
+  BagService,
+  BagVerifiable
+}
 import uk.ac.wellcome.platform.archive.common.storage.Resolvable
 import uk.ac.wellcome.platform.archive.common.storage.models._
 import uk.ac.wellcome.platform.archive.common.verify.Verification._
@@ -16,27 +19,30 @@ import scala.util.Try
 
 class BagVerifier()(
   implicit
-    bagService: BagService,
-    resolvable: Resolvable[ObjectLocation],
-    verifier: Verifier
+  bagService: BagService,
+  resolvable: Resolvable[ObjectLocation],
+  verifier: Verifier
 ) extends Logging {
 
   def verify(root: ObjectLocation) = Try {
     implicit val bagVerifiable = new BagVerifiable(root)
     val startTime = Instant.now()
 
     bagService.retrieve(root) match {
-      case Left(e) => IngestFailed(VerificationSummary.incomplete(root, e, startTime), e)
-      case Right(bag) => VerificationSummary.create(root, bag.verify, startTime) match {
-        case success@VerificationSuccessSummary(_, _, _, _) =>
-          IngestStepSucceeded(success)
-        case failure@VerificationFailureSummary(_, _, _, _) =>
-          IngestFailed(failure, InvalidBag(bag))
-        case incomplete@VerificationIncompleteSummary(_, _, _, _) =>
-          IngestFailed(incomplete, incomplete.e)
-      }
+      case Left(e) =>
+        IngestFailed(VerificationSummary.incomplete(root, e, startTime), e)
+      case Right(bag) =>
+        VerificationSummary.create(root, bag.verify, startTime) match {
+          case success @ VerificationSuccessSummary(_, _, _, _) =>
+            IngestStepSucceeded(success)
+          case failure @ VerificationFailureSummary(_, _, _, _) =>
+            IngestFailed(failure, InvalidBag(bag))
+          case incomplete @ VerificationIncompleteSummary(_, _, _, _) =>
+            IngestFailed(incomplete, incomplete.e)
+        }
     }
   }
 }
 
-case class InvalidBag(bag: Bag) extends Throwable(s"Invalid bag: ${bag.info.externalIdentifier}")
+case class InvalidBag(bag: Bag)
+    extends Throwable(s"Invalid bag: ${bag.info.externalIdentifier}")
diff --git a/...c/main/scala/uk/ac/wellcome/platform/archive/bagverifier/services/BagVerifierWorker.scala b/...c/main/scala/uk/ac/wellcome/platform/archive/bagverifier/services/BagVerifierWorker.scala
@@ -5,7 +5,10 @@ import com.amazonaws.services.sqs.AmazonSQSAsync
 import grizzled.slf4j.Logging
 import org.apache.commons.codec.digest.MessageDigestAlgorithms
 import uk.ac.wellcome.json.JsonUtil._
-import uk.ac.wellcome.messaging.sqsworker.alpakka.{AlpakkaSQSWorker, AlpakkaSQSWorkerConfig}
+import uk.ac.wellcome.messaging.sqsworker.alpakka.{
+  AlpakkaSQSWorker,
+  AlpakkaSQSWorkerConfig
+}
 import uk.ac.wellcome.messaging.worker.models.Result
 import uk.ac.wellcome.messaging.worker.monitoring.MonitoringClient
 import uk.ac.wellcome.platform.archive.bagverifier.models.VerificationSummary

diff --git a/...r/src/test/scala/uk/ac/wellcome/platform/archive/bagverifier/BagVerifierFeatureTest.scala b/...r/src/test/scala/uk/ac/wellcome/platform/archive/bagverifier/BagVerifierFeatureTest.scala
@@ -85,7 +85,6 @@ class BagVerifierFeatureTest
                       assertTopicReceivesIngestUpdates(
                         payload.ingestId,
                         ingestTopic) { ingestUpdates =>
-
                         debug(s"Got $ingestUpdates")
 
                         ingestUpdates.size shouldBe 2

diff --git a/...test/scala/uk/ac/wellcome/platform/archive/bagverifier/fixtures/BagVerifierFixtures.scala b/...test/scala/uk/ac/wellcome/platform/archive/bagverifier/fixtures/BagVerifierFixtures.scala
@@ -5,10 +5,19 @@ import uk.ac.wellcome.messaging.fixtures.SNS.Topic
 import uk.ac.wellcome.messaging.fixtures.SQS
 import uk.ac.wellcome.messaging.fixtures.SQS.Queue
 import uk.ac.wellcome.messaging.fixtures.worker.AlpakkaSQSWorkerFixtures
-import uk.ac.wellcome.platform.archive.bagverifier.services.{BagVerifier, BagVerifierWorker}
+import uk.ac.wellcome.platform.archive.bagverifier.services.{
+  BagVerifier,
+  BagVerifierWorker
+}
 import uk.ac.wellcome.platform.archive.common.bagit.services.BagService
-import uk.ac.wellcome.platform.archive.common.fixtures.{MonitoringClientFixture, OperationFixtures}
-import uk.ac.wellcome.platform.archive.common.storage.services.{S3ObjectVerifier, S3Resolvable}
+import uk.ac.wellcome.platform.archive.common.fixtures.{
+  MonitoringClientFixture,
+  OperationFixtures
+}
+import uk.ac.wellcome.platform.archive.common.storage.services.{
+  S3ObjectVerifier,
+  S3Resolvable
+}
 
 import scala.concurrent.ExecutionContext.Implicits.global
 

diff --git a/.../src/test/scala/uk/ac/wellcome/platform/archive/bagverifier/fixtures/VerifyFixtures.scala b/.../src/test/scala/uk/ac/wellcome/platform/archive/bagverifier/fixtures/VerifyFixtures.scala
@@ -1,7 +1,10 @@
 package uk.ac.wellcome.platform.archive.bagverifier.fixtures
 
 import uk.ac.wellcome.platform.archive.common.fixtures.RandomThings
-import uk.ac.wellcome.platform.archive.common.storage.services.{S3ObjectVerifier, S3Resolvable}
+import uk.ac.wellcome.platform.archive.common.storage.services.{
+  S3ObjectVerifier,
+  S3Resolvable
+}
 import uk.ac.wellcome.platform.archive.common.verify._
 import uk.ac.wellcome.storage.ObjectLocation
 import uk.ac.wellcome.storage.fixtures.S3

diff --git a/...src/test/scala/uk/ac/wellcome/platform/archive/bagverifier/services/BagVerifierTest.scala b/...src/test/scala/uk/ac/wellcome/platform/archive/bagverifier/services/BagVerifierTest.scala
@@ -3,11 +3,21 @@ package uk.ac.wellcome.platform.archive.bagverifier.services
 import org.scalatest.concurrent.ScalaFutures
 import org.scalatest.{FunSpec, Matchers, OptionValues, TryValues}
 import uk.ac.wellcome.platform.archive.bagverifier.fixtures.BagVerifierFixtures
-import uk.ac.wellcome.platform.archive.bagverifier.models.{VerificationFailureSummary, VerificationIncompleteSummary, VerificationSuccessSummary}
+import uk.ac.wellcome.platform.archive.bagverifier.models.{
+  VerificationFailureSummary,
+  VerificationIncompleteSummary,
+  VerificationSuccessSummary
+}
 import uk.ac.wellcome.platform.archive.common.bagit.services.BagUnavailable
-import uk.ac.wellcome.platform.archive.common.fixtures.{BagLocationFixtures, FileEntry}
+import uk.ac.wellcome.platform.archive.common.fixtures.{
+  BagLocationFixtures,
+  FileEntry
+}
 import uk.ac.wellcome.platform.archive.common.storage.LocationNotFound
-import uk.ac.wellcome.platform.archive.common.storage.models.{IngestFailed, IngestStepSucceeded}
+import uk.ac.wellcome.platform.archive.common.storage.models.{
+  IngestFailed,
+  IngestStepSucceeded
+}
 import uk.ac.wellcome.platform.archive.common.verify.FailedChecksumNoMatch
 
 class BagVerifierTest
@@ -190,7 +200,8 @@ class BagVerifierTest
             val error = summary.e
 
             error shouldBe a[BagUnavailable]
-            error.getMessage should include("Error loading tagmanifest-sha256.txt")
+            error.getMessage should include(
+              "Error loading tagmanifest-sha256.txt")
           }
       }
     }

diff --git a/...est/scala/uk/ac/wellcome/platform/archive/bagverifier/services/S3ObjectVerifierTest.scala b/...est/scala/uk/ac/wellcome/platform/archive/bagverifier/services/S3ObjectVerifierTest.scala
@@ -3,7 +3,10 @@ package uk.ac.wellcome.platform.archive.bagverifier.services
 import com.amazonaws.services.s3.model.PutObjectResult
 import org.scalatest.{EitherValues, FunSpec, Matchers}
 import uk.ac.wellcome.platform.archive.bagverifier.fixtures.VerifyFixture
-import uk.ac.wellcome.platform.archive.common.storage.{LocationError, LocationNotFound}
+import uk.ac.wellcome.platform.archive.common.storage.{
+  LocationError,
+  LocationNotFound
+}
 import uk.ac.wellcome.platform.archive.common.verify._
 import uk.ac.wellcome.storage.ObjectLocation
 

diff --git a/common/src/main/scala/uk/ac/wellcome/platform/archive/common/bagit/models/Bag.scala b/common/src/main/scala/uk/ac/wellcome/platform/archive/common/bagit/models/Bag.scala
@@ -1,8 +1,8 @@
 package uk.ac.wellcome.platform.archive.common.bagit.models
 
 case class Bag(
-                info: BagInfo,
-                manifest: BagManifest,
-                tagManifest: BagManifest,
-                fetch: Option[BagFetch] = None
-              )
+  info: BagInfo,
+  manifest: BagManifest,
+  tagManifest: BagManifest,
+  fetch: Option[BagFetch] = None
+)
diff --git a/common/src/main/scala/uk/ac/wellcome/platform/archive/common/bagit/models/BagFetch.scala b/common/src/main/scala/uk/ac/wellcome/platform/archive/common/bagit/models/BagFetch.scala
@@ -7,11 +7,11 @@ import scala.util.Try
 import scala.util.matching.Regex
 
 case class BagFetch(
-                     files: List[BagFetchEntry]
-                   )
-
+  files: List[BagFetchEntry]
+)
 
 object BagFetch {
+
   /** Read/write the contents of a Fetch File as defined by RFC 8493 § 2.2.3.
     *
     * Relevant notes: