Merge pull request #1536 from broadinstitute/update/minor_patch

CORE-69: Minor and patch updates - google-cloud-nio to 0.127.29 - scalafmt-core to 3.8.4 - sentry-logback to 7.20.0
broadinstitute · Jan 14, 2025 · 4466555 · 4466555
2 parents a28a386 + bca026f
commit 4466555
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -2,3 +2,6 @@
 
 # scalafmt mass change
 3686bb47a5b215733a46c3393a51e950fcaa635f
+
+# Scala Steward: Reformat with scalafmt 3.8.4
+c7a758f4143587c0355fee5580523cf7be0ead66
diff --git a/.scalafmt.conf b/.scalafmt.conf
@@ -1,4 +1,4 @@
-version = 3.8.3
+version = 3.8.4
 align = none
 align.openParenCallSite = true
 align.openParenDefnSite = true

diff --git a/automation/project/plugins.sbt b/automation/project/plugins.sbt
@@ -1 +1 @@
-logLevel := Level.Warn
+logLevel := Level.Warn
diff --git a/automation/src/test/scala/org/broadinstitute/dsde/test/LibraryData.scala b/automation/src/test/scala/org/broadinstitute/dsde/test/LibraryData.scala
@@ -13,35 +13,34 @@ object LibraryData {
     "library:RS-PD" -> false,
     "library:IRB" -> false,
     "library:RS-G" -> "N/A",
-    "library:NAGR" -> "No")
+    "library:NAGR" -> "No"
+  )
 
   val metadataBasic = Map(
-     "library:datasetName"->"name",
-     "library:datasetVersion"->"v1.0",
-     "library:datasetDescription"->"desc",
-     "library:datasetCustodian"->"cust",
-     "library:datasetDepositor"->"depo",
-     "library:contactEmail"->"name@example.com",
-     "library:datasetOwner"->"owner",
-     "library:institute"->Seq("inst","it","ute"),
-     "library:indication"->"indic",
-     "library:numSubjects"->123,
-     "library:projectName"->"proj",
-     "library:datatype"->Seq("data","type"),
-     "library:dataCategory"->Seq("data","category"),
-     "library:dataUseRestriction"->"dur",
-     "library:studyDesign"->"study",
-     "library:cellType"->"cell",
-     "library:requiresExternalApproval"->false,
-     "library:useLimitationOption"-> "skip",
-     "library:technology"->Seq("is an optional","array attribute"))
+    "library:datasetName" -> "name",
+    "library:datasetVersion" -> "v1.0",
+    "library:datasetDescription" -> "desc",
+    "library:datasetCustodian" -> "cust",
+    "library:datasetDepositor" -> "depo",
+    "library:contactEmail" -> "name@example.com",
+    "library:datasetOwner" -> "owner",
+    "library:institute" -> Seq("inst", "it", "ute"),
+    "library:indication" -> "indic",
+    "library:numSubjects" -> 123,
+    "library:projectName" -> "proj",
+    "library:datatype" -> Seq("data", "type"),
+    "library:dataCategory" -> Seq("data", "category"),
+    "library:dataUseRestriction" -> "dur",
+    "library:studyDesign" -> "study",
+    "library:cellType" -> "cell",
+    "library:requiresExternalApproval" -> false,
+    "library:useLimitationOption" -> "skip",
+    "library:technology" -> Seq("is an optional", "array attribute")
+  )
 
   // to set a discoverable by group, you can add the following with your specific group
   // "library:discoverableByGroups"->Seq("all_broad_users")
 
-   val metadataORSP = metadataBasic ++ Map(
-      "library:useLimitationOption"->"orsp",
-      "library:orsp"->"some orsp")
-
+  val metadataORSP = metadataBasic ++ Map("library:useLimitationOption" -> "orsp", "library:orsp" -> "some orsp")
 
 }
diff --git a/automation/src/test/scala/org/broadinstitute/dsde/test/api/orch/OrchestrationApiSpec.scala b/automation/src/test/scala/org/broadinstitute/dsde/test/api/orch/OrchestrationApiSpec.scala
@@ -1,6 +1,5 @@
 package org.broadinstitute.dsde.test.api.orch
 
-
 import akka.http.scaladsl.model.StatusCodes
 import org.broadinstitute.dsde.test.OrchConfig
 import org.broadinstitute.dsde.workbench.auth.AuthToken
@@ -18,19 +17,13 @@ import org.scalatest.time.{Minutes, Seconds, Span}
 import java.time.Instant
 import java.util.UUID
 
-
-class OrchestrationApiSpec
-  extends AnyFreeSpec
-    with Matchers
-    with ScalaFutures
-    with Eventually {
+class OrchestrationApiSpec extends AnyFreeSpec with Matchers with ScalaFutures with Eventually {
 
   implicit override val patienceConfig: PatienceConfig = PatienceConfig(timeout = scaled(Span(5, Seconds)))
   val billingAccountId: String = ServiceTestConfig.Projects.billingAccountId
 
-  def nowPrint(text: String): Unit = {
+  def nowPrint(text: String): Unit =
     println(s"${Instant.now} : $text")
-  }
 
   "Orchestration" - {
     "should link an eRA Commons account with access to the TARGET closed-access dataset" ignore {
@@ -51,14 +44,14 @@ class OrchestrationApiSpec
       finally resetNihLinkToInactive()
     }
 
-  "should link an eRA Commons account with access to none of the supported closed-access datasets" in {
-    val user = UserPool.chooseAuthDomainUser
-    implicit val userToken: AuthToken = user.makeAuthToken()
+    "should link an eRA Commons account with access to none of the supported closed-access datasets" in {
+      val user = UserPool.chooseAuthDomainUser
+      implicit val userToken: AuthToken = user.makeAuthToken()
 
-    Orchestration.NIH.addUserInNIH(OrchConfig.Users.genericJsonWebTokenKey)
-    try verifyDatasetPermissions(Set(NihDatasetPermission("TCGA", false), NihDatasetPermission("TARGET", false)))
-    finally resetNihLinkToInactive()
-  }
+      Orchestration.NIH.addUserInNIH(OrchConfig.Users.genericJsonWebTokenKey)
+      try verifyDatasetPermissions(Set(NihDatasetPermission("TCGA", false), NihDatasetPermission("TARGET", false)))
+      finally resetNihLinkToInactive()
+    }
 
     "should sync the whitelist and remove a user who no longer has access to either closed-access dataset" ignore {
       val user = UserPool.chooseAuthDomainUser
@@ -73,8 +66,8 @@ class OrchestrationApiSpec
     }
   }
 
-  //We need to reset the user's link to a state where it doesn't have access to any of the datasets
-  //To do so, we will link with a JWT that doesn't have access to any datasets and then sync both whitelists
+  // We need to reset the user's link to a state where it doesn't have access to any of the datasets
+  // To do so, we will link with a JWT that doesn't have access to any datasets and then sync both whitelists
   private def resetNihLinkToInactive()(implicit authToken: AuthToken) = {
     Orchestration.NIH.addUserInNIH(OrchConfig.Users.genericJsonWebTokenKey)
 
@@ -83,7 +76,9 @@ class OrchestrationApiSpec
     verifyDatasetPermissions(Set(NihDatasetPermission("TCGA", false), NihDatasetPermission("TARGET", false)))
   }
 
-  private def verifyDatasetPermissions(expectedPermissions: Set[NihDatasetPermission])(implicit authToken: AuthToken) = {
+  private def verifyDatasetPermissions(
+    expectedPermissions: Set[NihDatasetPermission]
+  )(implicit authToken: AuthToken) = {
     // Sam caches group membership for a minute (but not in fiab) so may need to wait
     implicit val patienceConfig = PatienceConfig(Span(2, Minutes), Span(10, Seconds))
     eventually {

diff --git a/automation/src/test/scala/org/broadinstitute/dsde/test/api/orch/PublishedWorkspaceSpec.scala b/automation/src/test/scala/org/broadinstitute/dsde/test/api/orch/PublishedWorkspaceSpec.scala
@@ -15,15 +15,10 @@ import org.scalatest.matchers.should.Matchers
 import org.scalatest.time.{Seconds, Span}
 import spray.json._
 
+class PublishedWorkspaceSpec extends AnyFreeSpec with WorkspaceFixtures with Matchers with Eventually with RandomUtil {
 
-class PublishedWorkspaceSpec
-  extends AnyFreeSpec
-    with WorkspaceFixtures
-    with Matchers
-    with Eventually
-    with RandomUtil {
-
-  implicit override val patienceConfig: PatienceConfig = PatienceConfig(timeout = scaled(Span(30, Seconds)), interval = scaled(Span(2, Seconds)))
+  implicit override val patienceConfig: PatienceConfig =
+    PatienceConfig(timeout = scaled(Span(30, Seconds)), interval = scaled(Span(2, Seconds)))
   val billingAccountId: String = ServiceTestConfig.Projects.billingAccountId
 
   "a user with publish permissions" - {
@@ -36,7 +31,6 @@ class PublishedWorkspaceSpec
 
         withTemporaryBillingProject(billingAccountId, users = List(curatorUser.email).some) { billingProject =>
           withWorkspace(billingProject, "PublishedWorkspaceSpec_workspace") { workspaceName =>
-
             val data = LibraryData.metadataBasic + ("library:datasetName" -> workspaceName)
             Orchestration.library.setLibraryAttributes(billingProject, workspaceName, data)
             Orchestration.library.publishWorkspace(billingProject, workspaceName)
@@ -86,8 +80,7 @@ class PublishedWorkspaceSpec
                     isVisibleInLibrary(clonedWorkspaceName) shouldBe false
                   }
                 }
-              }
-              finally Orchestration.workspaces.delete(billingProject, clonedWorkspaceName)
+              } finally Orchestration.workspaces.delete(billingProject, clonedWorkspaceName)
             }
           }(UserPool.chooseProjectOwner.makeAuthToken(billingScopes))
         }
@@ -106,16 +99,18 @@ class PublishedWorkspaceSpec
 
               val clonedWorkspaceName = workspaceName + "_clone"
               Orchestration.workspaces.clone(billingProject, workspaceName, billingProject, clonedWorkspaceName)
-              try {
-                //Verify default group "All users"
-                //In swagger you make sure that getDiscoverableGroup endpoint shows []
-                withClue(s"Get api/library/${billingProject}/${clonedWorkspaceName}/discoverableGroups endpoint shows []") {
+              try
+                // Verify default group "All users"
+                // In swagger you make sure that getDiscoverableGroup endpoint shows []
+                withClue(
+                  s"Get api/library/${billingProject}/${clonedWorkspaceName}/discoverableGroups endpoint shows []"
+                ) {
                   eventually {
-                    val accessGroup: Seq[String] = Orchestration.library.getDiscoverableGroups(billingProject, clonedWorkspaceName)
+                    val accessGroup: Seq[String] =
+                      Orchestration.library.getDiscoverableGroups(billingProject, clonedWorkspaceName)
                     accessGroup.size shouldBe 0
                   }
                 }
-              }
               finally Orchestration.workspaces.delete(billingProject, clonedWorkspaceName)
             }
           }(UserPool.chooseProjectOwner.makeAuthToken(billingScopes))
@@ -130,7 +125,6 @@ class PublishedWorkspaceSpec
 
         withTemporaryBillingProject(billingAccountId, users = List(curatorUser.email).some) { billingProject =>
           withWorkspace(billingProject, "PublishedWorkspaceSpec_consentcodes") { workspaceName =>
-
             val data = LibraryData.metadataBasic + ("library:datasetName" -> workspaceName) ++ LibraryData.consentCodes
             Orchestration.library.setLibraryAttributes(billingProject, workspaceName, data)
             Orchestration.library.publishWorkspace(billingProject, workspaceName)
@@ -153,7 +147,6 @@ class PublishedWorkspaceSpec
 
         withTemporaryBillingProject(billingAccountId, users = List(curatorUser.email).some) { billingProject =>
           withWorkspace(billingProject, "PublishedWorkspaceSpec_tags", attributes = Some(tags)) { workspaceName =>
-
             val data = LibraryData.metadataBasic + ("library:datasetName" -> workspaceName)
             Orchestration.library.setLibraryAttributes(billingProject, workspaceName, data)
             Orchestration.library.publishWorkspace(billingProject, workspaceName)
@@ -170,7 +163,6 @@ class PublishedWorkspaceSpec
     }
   }
 
-
   /**
     *
     * @return True: workspace is visible in library table
@@ -182,7 +174,9 @@ class PublishedWorkspaceSpec
     total == 1
   }
 
-  private def getDatasetFieldValues(workspaceName: String, fieldName: String)(implicit token: AuthToken): List[String] = {
+  private def getDatasetFieldValues(workspaceName: String,
+                                    fieldName: String
+  )(implicit token: AuthToken): List[String] = {
     import DefaultJsonProtocol._
     val datasetMap: String = Orchestration.library.searchPublishedLibraryDataset(workspaceName)
     val results: JsValue = datasetMap.parseJson.asJsObject.fields("results")

diff --git a/...hmarks/src/main/scala/org/broadinstitute/dsde/firecloud/utils/TsvFormatterBenchmark.scala b/...hmarks/src/main/scala/org/broadinstitute/dsde/firecloud/utils/TsvFormatterBenchmark.scala
@@ -45,9 +45,10 @@ object TsvFormatterBenchmark {
           AttributeName.withDefaultNS("col2") -> AttributeBoolean(true),
           AttributeName.withDefaultNS("fourth") -> AttributeNumber(-123.45),
           AttributeName.withDefaultNS("last") -> AttributeValueList(
-            Seq(AttributeString("gs://some-bucket/somefile1.ext"),
-                AttributeString("gs://some-bucket/somefile2.ext"),
-                AttributeString("gs://some-bucket/somefile3.ext")
+            Seq(
+              AttributeString("gs://some-bucket/somefile1.ext"),
+              AttributeString("gs://some-bucket/somefile2.ext"),
+              AttributeString("gs://some-bucket/somefile3.ext")
             )
           )
         )

diff --git a/project/Dependencies.scala b/project/Dependencies.scala
@@ -44,7 +44,7 @@ object Dependencies {
     // elasticsearch requires log4j, but we redirect log4j to logback
     "org.apache.logging.log4j"       % "log4j-to-slf4j"      % "2.24.3",
     "ch.qos.logback"                 % "logback-classic"     % "1.5.16",
-    "io.sentry"                      % "sentry-logback"      % "7.19.1",
+    "io.sentry"                      % "sentry-logback"      % "7.20.0",
     "com.typesafe.scala-logging"    %% "scala-logging"       % "3.9.5",
 
     "org.parboiled" % "parboiled-core" % "1.4.1",
@@ -96,7 +96,7 @@ object Dependencies {
     "org.scalatest"                 %% "scalatest"           % "3.2.19"   % "test",
     "org.mock-server"                % "mockserver-netty-no-dependencies"    % "5.15.0"  % "test",
     // provides testing mocks
-    "com.google.cloud"               % "google-cloud-nio"    % "0.127.28" % "test",
+    "com.google.cloud"               % "google-cloud-nio"    % "0.127.29" % "test",
     "org.scalatestplus"             %% "mockito-4-5"         % "3.2.12.0" % "test"
   )
 }
diff --git a/project/Merging.scala b/project/Merging.scala
@@ -1,9 +1,9 @@
 import sbtassembly.{MergeStrategy, PathList}
 
 object Merging {
-  def customMergeStrategy(oldStrategy: (String) => MergeStrategy):(String => MergeStrategy) = {
+  def customMergeStrategy(oldStrategy: (String) => MergeStrategy): (String => MergeStrategy) = {
     case x if x.endsWith("io.netty.versions.properties") => MergeStrategy.discard
-    case x if x.contains("native-image/io.netty") => MergeStrategy.first
+    case x if x.contains("native-image/io.netty")        => MergeStrategy.first
 
     // TODO: we no longer target Java 8, reassess this:
     // we target Java 8, which does not use module-info.class. Some dependencies (Jackson) cause assembly problems on module-info
@@ -12,19 +12,19 @@ object Merging {
     case x if x.contains("javax/activation") => MergeStrategy.first
     case x if x.contains("javax/annotation") => MergeStrategy.first
 
-    case x if x.endsWith("kotlin-stdlib.kotlin_module") => MergeStrategy.first
-    case x if x.contains("bouncycastle") => MergeStrategy.first
+    case x if x.endsWith("kotlin-stdlib.kotlin_module")        => MergeStrategy.first
+    case x if x.contains("bouncycastle")                       => MergeStrategy.first
     case x if x.endsWith("kotlin-stdlib-common.kotlin_module") => MergeStrategy.first
-    case x if x.endsWith("okio.kotlin_module") => MergeStrategy.first
-    case x if x.endsWith("arrow-git.properties") => MergeStrategy.concat
+    case x if x.endsWith("okio.kotlin_module")                 => MergeStrategy.first
+    case x if x.endsWith("arrow-git.properties")               => MergeStrategy.concat
 
     // For the following error:
     // Error: (assembly) deduplicate: different file contents found in the following:
     // Error: /home/sbtuser/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/protobuf/protobuf-java/3.19.4/protobuf-java-3.19.4.jar:google/protobuf/struct.proto
     // Error: /home/sbtuser/.cache/coursier/v1/https/repo1.maven.org/maven2/com/typesafe/akka/akka-protobuf-v3_2.13/2.6.19/akka-protobuf-v3_2.13-2.6.19.jar:google/protobuf/struct.proto
-    case PathList("google", "protobuf", _ @ _*) => MergeStrategy.first
+    case PathList("google", "protobuf", _ @_*)                            => MergeStrategy.first
     case PathList("META-INF", "versions", "9", "OSGI-INF", "MANIFEST.MF") => MergeStrategy.first
-    case PathList("META-INF", "spring", "aot.factories") => MergeStrategy.first
-    case x => oldStrategy(x)
+    case PathList("META-INF", "spring", "aot.factories")                  => MergeStrategy.first
+    case x                                                                => oldStrategy(x)
   }
 }
diff --git a/project/Testing.scala b/project/Testing.scala
@@ -8,7 +8,6 @@ object Testing {
   lazy val IntegrationTest = config("it") extend Test
 
   val commonTestSettings: Seq[Setting[_]] = List(
-
     Test / testOptions ++= Seq(Tests.Filter(s => !isIntegrationTest(s))),
     Test / testOptions += Tests.Argument("-oD"), // D = individual test durations
     IntegrationTest / testOptions := Seq(Tests.Filter(s => isIntegrationTest(s))),
@@ -17,16 +16,15 @@ object Testing {
     // However, we've already initialized Netty elsewhere (mockserver, I assume),
     // so the call fails. Tell ES to skip attempting to set this value.
     Test / javaOptions += "-Des.set.netty.runtime.available.processors=false",
-
     Test / fork := true,
     Test / parallelExecution := false,
-    IntegrationTest / fork := false, // allow easy overriding of conf values via system props
+    IntegrationTest / fork := false // allow easy overriding of conf values via system props
 
   )
 
   implicit class ProjectTestSettings(val project: Project) extends AnyVal {
     def withTestSettings: Project = project
-      .configs(IntegrationTest).settings(inConfig(IntegrationTest)(Defaults.testTasks): _*)
+      .configs(IntegrationTest)
+      .settings(inConfig(IntegrationTest)(Defaults.testTasks): _*)
   }
 }
-
diff --git a/project/Version.scala b/project/Version.scala
@@ -7,10 +7,10 @@ object Version {
   val baseModelVersion = "0.1"
 
   def getVersionString = {
-    def getLastModelCommitFromGit = { s"""git rev-parse --short HEAD""" !! }
+    def getLastModelCommitFromGit = s"""git rev-parse --short HEAD""" !!
 
     // either specify git model hash as an env var or derive it
-    val lastModelCommit = sys.env.getOrElse("GIT_MODEL_HASH", getLastModelCommitFromGit ).trim()
+    val lastModelCommit = sys.env.getOrElse("GIT_MODEL_HASH", getLastModelCommitFromGit).trim()
     val version = baseModelVersion + "-" + lastModelCommit
 
     // The project isSnapshot string passed in via command line settings, if desired.

diff --git a/src/main/scala/org/broadinstitute/dsde/firecloud/webservice/LibraryApiService.scala b/src/main/scala/org/broadinstitute/dsde/firecloud/webservice/LibraryApiService.scala
@@ -93,11 +93,10 @@ trait LibraryApiService
                         }
                       }
                     }
-                  } ~ {
+                  } ~
                     get {
                       complete(libraryServiceConstructor(userInfo).getLibraryMetadata(namespace, name))
                     }
-                  }
                 } ~
                   path("discoverableGroups") {
                     put {

diff --git a/src/test/scala/org/broadinstitute/dsde/firecloud/EntityServiceSpec.scala b/src/test/scala/org/broadinstitute/dsde/firecloud/EntityServiceSpec.scala
@@ -279,15 +279,12 @@ class EntityServiceSpec extends BaseServiceSpec with BeforeAndAfterEach {
   }
 
   "EntityService.importJob" - {
-    "should send tdrexport to cWDS" in {
+    "should send tdrexport to cWDS" in
       importJobTestImpl(importFiletype = "tdrexport")
-    }
-    "should send pfb to cWDS" in {
+    "should send pfb to cWDS" in
       importJobTestImpl(importFiletype = "pfb")
-    }
-    "should send rawlsjson to cWDS" in {
+    "should send rawlsjson to cWDS" in
       importJobTestImpl(importFiletype = "rawlsjson")
-    }
 
     def importJobTestImpl(importFiletype: String) = {
       // set up mocks
-Original file line number
+Diff line change
@@ Expand Up / @@ -93,11 +93,10 @@ trait LibraryApiService @@
                             }
                           }
                         }
-                      } ~ {
+                      } ~
                         get {
                           complete(libraryServiceConstructor(userInfo).getLibraryMetadata(namespace, name))
                         }
-                      }
                     } ~
                       path("discoverableGroups") {
                         put {
@@ Expand Down @@