CORE-69: Minor and patch updates - commons-codec to 1.17.2 - azure-identity to 1.15.0 - billing-profile-manager-client to 0.1.598-SNAPSHOT - sentry-logback to 7.20.0 - workspace-manager-client to 0.254.1170-SNAPSHOT - google-cloud-nio to 0.127.29 - jersey-jnh-connector to 3.1.10 - scalafmt-core to 3.8.4

.git-blame-ignore-revs

@@ -32,3 +32,6 @@ f5916aefb603a97498617785baa46bf5cf9e3164
 
 # Scala Steward: Reformat with scalafmt 3.8.3
 4ff2c5aaf0cd1acfbf510d0ffc9391849c16e9e3
+
+# Scala Steward: Reformat with scalafmt 3.8.4
+1381b307683c6b0a9db4e2fe94a5819b520d7253

.github/workflows/format.yaml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-
+      - uses: sbt/setup-sbt@v1
       - uses: actions/checkout@v4
         with:
           fetch-depth: 2

.github/workflows/test.yml

@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+      - uses: sbt/setup-sbt@v1
 
       - uses: actions/checkout@v4
 

.scalafmt.conf

@@ -1,4 +1,4 @@
-version = 3.8.3
+version = 3.8.4
 align = none
 align.openParenCallSite = true
 align.openParenDefnSite = true

automation/src/test/scala/org/broadinstitute/dsde/test/api/WorkspaceApiSpec.scala

@@ -319,7 +319,7 @@ class WorkspaceApiSpec
         "workspaceName" -> Map("namespace" -> projectName, "name" -> destWorkspaceName)
       )
 
-      "to import method configs from another workspace" in {
+      "to import method configs from another workspace" in
         withTemporaryBillingProject(billingAccountId) { projectName =>
           withWorkspace(projectName,
                         prependUUID("reader-import-config-dest-workspace"),
@@ -358,9 +358,8 @@ class WorkspaceApiSpec
             }(ownerAuthToken)
           }(ownerAuthToken)
         }(owner.makeAuthToken(billingScopes))
-      }
 
-      "to import method configs from the method repo" in {
+      "to import method configs from the method repo" in
         withTemporaryBillingProject(billingAccountId) { projectName =>
           withWorkspace(projectName,
                         prependUUID("reader-import-config-dest-workspace"),
@@ -394,7 +393,6 @@ class WorkspaceApiSpec
             }(ownerAuthToken)
           }(ownerAuthToken)
         }(owner.makeAuthToken(billingScopes))
-      }
     }
   }
 

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

@@ -43,7 +43,10 @@ class BillingProjectDeletion(
     for {
       _ <- billingRepository.deleteBillingProject(projectName)
       _ <- samDAO
-        .deleteResource(SamResourceTypeNames.billingProject, projectName.value, ctx) recoverWith { // Moving this to the end so that the rawls record is cleared even if there are issues clearing the Sam resource (theoretical workaround for https://broadworkbench.atlassian.net/browse/CA-1206)
+        .deleteResource(SamResourceTypeNames.billingProject,
+                        projectName.value,
+                        ctx
+        ) recoverWith { // Moving this to the end so that the rawls record is cleared even if there are issues clearing the Sam resource (theoretical workaround for https://broadworkbench.atlassian.net/browse/CA-1206)
         case t: Throwable =>
           logger.warn(
             s"Unexpected failure deleting billing project (while deleting billing project in Sam) for billing project `${projectName.value}`",

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

@@ -589,8 +589,8 @@ class HttpGoogleServicesDAO(val clientSecrets: GoogleClientSecrets,
       firecloudHasAccess <- testTerraBillingAccountAccess(billingAccount)
       userHasAccess <- cred.traverse(c => testBillingAccountAccess(billingAccount, c))
     } yield
-    // Return false if the user does not have a Google token
-    firecloudHasAccess && userHasAccess.getOrElse(false)
+      // Return false if the user does not have a Google token
+      firecloudHasAccess && userHasAccess.getOrElse(false)
   }
 
   protected def testBillingAccountAccess(billingAccount: RawlsBillingAccountName, credential: Credential)(implicit

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

@@ -120,13 +120,12 @@ class ShardedHttpExecutionServiceCluster(readMembers: Set[ClusterMember],
                                                 userInfo: UserInfo
   ): Unit = {
     // execute but don't wait for completion
-    val labelFutureToIgnore = Future.traverse(parseSubWorkflowIdsFromMetadata(parentWorkflowMetadata)) {
-      subWorkflowId =>
-        retryUntilSuccessOrTimeout(failureLogMessage =
-          s"error patching label on workflow [$subWorkflowId], submission [$submissionId]"
-        )(2 seconds, 10 seconds) { () =>
-          getMember(executionServiceId).dao.patchLabels(subWorkflowId, userInfo, Map(SUBMISSION_ID_KEY -> submissionId))
-        }
+    val labelFutureToIgnore = Future.traverse(parseSubWorkflowIdsFromMetadata(parentWorkflowMetadata)) { subWorkflowId =>
+      retryUntilSuccessOrTimeout(failureLogMessage =
+        s"error patching label on workflow [$subWorkflowId], submission [$submissionId]"
+      )(2 seconds, 10 seconds) { () =>
+        getMember(executionServiceId).dao.patchLabels(subWorkflowId, userInfo, Map(SUBMISSION_ID_KEY -> submissionId))
+      }
     }
   }
 

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

@@ -1168,9 +1168,8 @@ trait EntityComponent {
     // perform actual deletion (not hiding) of all entities in a workspace
 
     def deleteFromDb(workspaceContext: Workspace): WriteAction[Int] =
-      EntityDependenciesDeletionQuery.deleteAction(workspaceContext) andThen {
+      EntityDependenciesDeletionQuery.deleteAction(workspaceContext) andThen
         filter(_.workspaceId === workspaceContext.workspaceIdAsUUID).delete
-      }
 
     def countReferringEntitiesForType(workspaceContext: Workspace, entityType: String): ReadAction[Int] =
       EntityAndAttributesRawSqlQuery.countReferencesToType(workspaceContext, entityType).map(_.sum)

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

@@ -481,15 +481,14 @@ trait RawlsBillingProjectComponent {
         // - to keep an audit log of billing account changes
         _ <- DBIO.sequence(billingProjects.map { project =>
           // ignore all currently-outstanding changes for this project
-          BillingAccountChanges.ignoreAllOutstanding(project.projectName) andThen {
+          BillingAccountChanges.ignoreAllOutstanding(project.projectName) andThen
             // insert the most recent change for this project
             BillingAccountChanges.create(
               project.projectName,
               project.billingAccount,
               billingAccount,
               userSubjectId
             )
-          }
         })
       } yield count
   }

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

@@ -675,15 +675,14 @@ trait SubmissionComponent {
           deleteSubmissionAttributes("WORKFLOW", "workflow_id"),
           deleteFromTable("WORKFLOW_MESSAGE", "WORKFLOW", "workflow_id"),
           deleteFromTable("SUBMISSION_VALIDATION", "WORKFLOW", "workflow_id")
-        ) andThen {
+        ) andThen
           DBIO.sequence(Seq("WORKFLOW") map { workflow_table =>
             // delete workflows
             sqlu"""delete w from #$workflow_table w
                    inner join SUBMISSION s on w.submission_id=s.id
                    where s.workspace_id=$workspaceId
             """
           })
-        }
       }
     }
 

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

@@ -53,9 +53,8 @@ trait WorkspaceFeatureFlagComponent {
     def listFlagsForWorkspace(workspaceId: UUID,
                               flags: List[WorkspaceFeatureFlag]
     ): ReadAction[Seq[WorkspaceFeatureFlag]] =
-      filter(flag => flag.workspaceId === workspaceId && flag.flagName.inSetBind(flags.map(_.name))).result.map {
-        recs =>
-          recs.map(rec => WorkspaceFeatureFlag(rec.flagName))
+      filter(flag => flag.workspaceId === workspaceId && flag.flagName.inSetBind(flags.map(_.name))).result.map { recs =>
+        recs.map(rec => WorkspaceFeatureFlag(rec.flagName))
       }
 
     def deleteAllForWorkspace(workspaceId: UUID): ReadWriteAction[Int] =

core/src/main/scala/org/broadinstitute/dsde/rawls/entities/datarepo/DataRepoEntityProvider.scala

@@ -133,8 +133,8 @@ class DataRepoEntityProvider(snapshotModel: SnapshotModel,
       // execute the query against BQ
       queryResults <- runBigQuery(queryConfigBuilder, petKey, GoogleProject(googleProject.value))
     } yield
-    // translate the BQ results into a single Rawls Entity
-    queryResultsToEntity(queryResults, entityType, pk)
+      // translate the BQ results into a single Rawls Entity
+      queryResultsToEntity(queryResults, entityType, pk)
     resultIO.unsafeToFuture()
   }
 
@@ -210,8 +210,8 @@ class DataRepoEntityProvider(snapshotModel: SnapshotModel,
         // execute the query against BQ
         queryResults <- runBigQuery(queryConfigBuilder, petKey, GoogleProject(googleProject.value))
       } yield
-      // translate the BQ results into a Rawls query result
-      queryResultsToEntities(queryResults, entityType, pk)
+        // translate the BQ results into a Rawls query result
+        queryResultsToEntities(queryResults, entityType, pk)
       resultIO.unsafeToFuture()
     }
 

core/src/main/scala/org/broadinstitute/dsde/rawls/expressions/parser/antlr/OutputExpressionValidationVisitor.scala

@@ -29,9 +29,9 @@ class OutputExpressionValidationVisitor
       aggregate <- aggregateT
       nextResult <- nextResultT
     } yield
-    // return whichever of aggregate and nextResult is bound
-    if (aggregate(AttributeNull) == UnboundOutputExpression) nextResult
-    else aggregate
+      // return whichever of aggregate and nextResult is bound
+      if (aggregate(AttributeNull) == UnboundOutputExpression) nextResult
+      else aggregate
 
   override def visitRelation(ctx: RelationContext): Try[Attribute => OutputExpression] =
     Failure(new RawlsException("Entity references not permitted in the middle of output expressions"))

core/src/main/scala/org/broadinstitute/dsde/rawls/methods/MethodConfigurationService.scala

@@ -363,21 +363,18 @@ class MethodConfigurationService(
     getV2WorkspaceContextAndPermissions(methodRepoQuery.source.workspaceName, SamWorkspaceActions.read) flatMap {
       workspaceContext =>
         dataSource.inTransaction { dataAccess =>
-          withMethodConfig(workspaceContext,
-                           methodRepoQuery.source.namespace,
-                           methodRepoQuery.source.name,
-                           dataAccess
-          ) { methodConfig =>
-            DBIO.from(
-              methodRepoDAO.postMethodConfig(
-                methodRepoQuery.methodRepoNamespace,
-                methodRepoQuery.methodRepoName,
-                methodConfig.copy(namespace = methodRepoQuery.methodRepoNamespace,
-                                  name = methodRepoQuery.methodRepoName
-                ),
-                ctx.userInfo
+          withMethodConfig(workspaceContext, methodRepoQuery.source.namespace, methodRepoQuery.source.name, dataAccess) {
+            methodConfig =>
+              DBIO.from(
+                methodRepoDAO.postMethodConfig(
+                  methodRepoQuery.methodRepoNamespace,
+                  methodRepoQuery.methodRepoName,
+                  methodConfig.copy(namespace = methodRepoQuery.methodRepoNamespace,
+                                    name = methodRepoQuery.methodRepoName
+                  ),
+                  ctx.userInfo
+                )
               )
-            )
           }
         }
     }

core/src/main/scala/org/broadinstitute/dsde/rawls/webservice/RawlsApiService.scala

@@ -147,7 +147,9 @@ trait RawlsApiService
 
   def apiRoutes =
     options(complete(OK)) ~
-      withExecutionContext(ExecutionContext.global) { // Serve real work off the global EC to free up the dispatcher to run more routes, including status
+      withExecutionContext(
+        ExecutionContext.global
+      ) { // Serve real work off the global EC to free up the dispatcher to run more routes, including status
         traceRequests(baseApiRoutes)
       }
 

core/src/main/scala/org/broadinstitute/dsde/rawls/workspace/WorkspaceService.scala

@@ -243,8 +243,8 @@ class WorkspaceService(
           getV2WorkspaceContextAndPermissions(workspaceName, SamWorkspaceActions.read, Option(options.attrSpecs))
         workspaceResponse <- getWorkspaceDetails(workspace, options, userProject)
       } yield
-      // post-process JSON to remove calculated-but-undesired keys
-      deepFilterJsObject(workspaceResponse.toJson.asJsObject, options.options)
+        // post-process JSON to remove calculated-but-undesired keys
+        deepFilterJsObject(workspaceResponse.toJson.asJsObject, options.options)
     )
   }
 
@@ -259,8 +259,8 @@ class WorkspaceService(
           getV2WorkspaceContextAndPermissionsById(workspaceId, SamWorkspaceActions.read, Option(options.attrSpecs))
         workspaceResponse <- getWorkspaceDetails(workspace, options, userProject)
       } yield
-      // post-process JSON to remove calculated-but-undesired keys
-      deepFilterJsObject(workspaceResponse.toJson.asJsObject, options.options)
+        // post-process JSON to remove calculated-but-undesired keys
+        deepFilterJsObject(workspaceResponse.toJson.asJsObject, options.options)
     )
   }
 

core/src/test/scala/org/broadinstitute/dsde/rawls/dataaccess/HttpExecutionServiceDAOSpec.scala

@@ -179,7 +179,7 @@ class HttpExecutionServiceDAOSpec
     }
   }
 
-  it should "get the version" in {
+  it should "get the version" in
     withStatsD {
       val result = test.version.futureValue
       result.cromwell shouldBe "25"
@@ -191,6 +191,5 @@ class HttpExecutionServiceDAOSpec
                                                                                Option(Subsystems.Cromwell)
       ))
     }
-  }
 
 }

core/src/test/scala/org/broadinstitute/dsde/rawls/dataaccess/HttpSamDAOSpec.scala

@@ -77,11 +77,12 @@ class HttpSamDAOSpec
                      1 minute
       )
     assertResult(SamDAO.NotUser) {
-      Await.result(dao.getUserIdInfo(
-                     "[email protected]",
-                     RawlsRequestContext(UserInfo(RawlsUserEmail(""), OAuth2BearerToken(""), 0, RawlsUserSubjectId("")))
-                   ),
-                   Duration.Inf
+      Await.result(
+        dao.getUserIdInfo(
+          "[email protected]",
+          RawlsRequestContext(UserInfo(RawlsUserEmail(""), OAuth2BearerToken(""), 0, RawlsUserSubjectId("")))
+        ),
+        Duration.Inf
       )
     }
   }

core/src/test/scala/org/broadinstitute/dsde/rawls/dataaccess/SubmissionCostServiceSpec.scala

@@ -167,7 +167,7 @@ class SubmissionCostServiceSpec extends AnyFlatSpec with RawlsTestUtils {
     `SubmissionCostService#executeWorkflowCostQuery` passes other values to `startParameterizedQuery`, so
     an exception will be thrown if a call is made to BigQuery in this case.
    */
-  it should "bypass BigQuery with no workflow IDs" in {
+  it should "bypass BigQuery with no workflow IDs" in
     assertResult(Map.empty) {
       Await.result(
         submissionCostService.getSubmissionCosts("submission-id",
@@ -179,5 +179,4 @@ class SubmissionCostServiceSpec extends AnyFlatSpec with RawlsTestUtils {
         1 minute
       )
     }
-  }
 }

core/src/test/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/AttributeComponentSpec.scala

@@ -1915,9 +1915,8 @@ class AttributeComponentSpec
     attributeTestData.combinations(2).flatMap(x => List(x, x.reverse)).foreach {
       case List(AttributeTestData(description1, attribute1), AttributeTestData(description2, attribute2)) =>
         it should s"reflect ${attributeTestFunction.description} changes in " +
-          s"a new attribute when $description1 changes to $description2" in {
-            attributeTestFunction.run(attribute1, attribute2)
-          }
+          s"a new attribute when $description1 changes to $description2" in
+          attributeTestFunction.run(attribute1, attribute2)
       case x =>
         throw new Exception(s"${x} is unexpected")
     }

core/src/test/scala/org/broadinstitute/dsde/rawls/dataaccess/slick/AttributeShardingSpec.scala

@@ -40,9 +40,8 @@ class AttributeShardingSpec
   )
 
   uuidCases foreach { case (uuidString, expectedShardId) =>
-    it should s"calculate shardId for UUID('$uuidString') correctly" in {
+    it should s"calculate shardId for UUID('$uuidString') correctly" in
       assertResult(expectedShardId)(determineShard(UUID.fromString(uuidString)))
-    }
   }
 
 }