CORE-69: Minor and patch updates - grpc-core to 1.78.0 - sbt-scoverage to 2.4.3 - scala-library to 2.13.18 - sbt-scalafmt to 2.5.6 - terra-common-lib to 1.1.68-SNAPSHOT - reactor-netty to 1.2.13 - google-cloud-nio to 0.128.9 - commons-codec to 1.20.0 - logback-classic to 1.5.23 - terra-cloud-resource-lib to 1.2.42-SNAPSHOT - scalafmt-core to 3.8.6 - sbt-scalafix to 0.14.5 - okio to 3.16.4

.github/workflows/verify_consumer_pacts.yml

@@ -321,7 +321,7 @@ jobs:
                           -e JANITOR_CLIENT_CREDENTIAL_FILE_PATH="" \
                           -e JANITOR_TRACK_RESOURCE_PROJECT_ID="" \
                           -e JANITOR_TRACK_RESOURCE_TOPIC_ID="" \
-                          sbtscala/scala-sbt:eclipse-temurin-17.0.15_6_1.11.7_2.13.17 \
+                          sbtscala/scala-sbt:eclipse-temurin-17.0.15_6_1.11.7_2.13.18 \
                           bash -c "git config --global --add safe.directory /working/sam && sbt \"set scalafmtOnCompile := false\" \"project pact4s\" \"testOnly *SamProviderSpec\""
 
   can-i-deploy: # The can-i-deploy job will run as a result of a Sam PR. It reports the pact verification statuses on all deployed environments.

automation/project/Settings.scala

@@ -41,7 +41,7 @@ object Settings {
   val commonSettings =
     commonBuildSettings ++ testSettings ++ List(
       organization := "org.broadinstitute.dsde.firecloud",
-      scalaVersion := "2.13.17",
+      scalaVersion := "2.13.18",
       resolvers ++= commonResolvers,
       scalacOptions ++= commonCompilerSettings
     )

project/Dependencies.scala

@@ -20,8 +20,8 @@ object Dependencies {
   val workbenchNotificationsV = s"1.1-$workbenchLibV"
   val workbenchOauth2V = s"0.9-$workbenchLibV"
   val monocleVersion = "2.0.5"
-  val crlVersion = "1.2.41-SNAPSHOT"
-  val tclVersion = "1.1.53-SNAPSHOT"
+  val crlVersion = "1.2.42-SNAPSHOT"
+  val tclVersion = "1.1.68-SNAPSHOT"
   val slf4jVersion = "2.0.6"
 
   val excludeAkkaActor = ExclusionRule(organization = "com.typesafe.akka", name = "akka-actor_2.12")
@@ -47,7 +47,7 @@ object Dependencies {
   val jacksonCore: ModuleID = "com.fasterxml.jackson.core" % "jackson-core" % jacksonV
 
   val logstashLogback: ModuleID = "net.logstash.logback" % "logstash-logback-encoder" % "9.0"
-  val logbackClassic: ModuleID = "ch.qos.logback" % "logback-classic" % "1.5.19"
+  val logbackClassic: ModuleID = "ch.qos.logback" % "logback-classic" % "1.5.23"
 
   val ravenLogback: ModuleID = "com.getsentry.raven" % "raven-logback" % "7.8.6"
   val scalaLogging: ModuleID = "com.typesafe.scala-logging" %% "scala-logging" % scalaLoggingV
@@ -65,11 +65,11 @@ object Dependencies {
   val akkaHttpTestKit: ModuleID = "com.typesafe.akka" %% "akka-http-testkit" % akkaHttpV % "test"
   val scalaCheck: ModuleID = "org.scalacheck" %% "scalacheck" % scalaCheckV % "test"
 
-  val reactorNetty: ModuleID = "io.projectreactor.netty" % "reactor-netty" % "1.2.10"
+  val reactorNetty: ModuleID = "io.projectreactor.netty" % "reactor-netty" % "1.2.13"
   val nettyAll: ModuleID = "io.netty" % "netty-all" % "4.2.7.Final"
 
   val excludIoGrpc = ExclusionRule(organization = "io.grpc", name = "grpc-core")
-  val ioGrpc: ModuleID = "io.grpc" % "grpc-core" % "1.75.0"
+  val ioGrpc: ModuleID = "io.grpc" % "grpc-core" % "1.78.0"
 
   val googleOAuth2: ModuleID = "com.google.auth" % "google-auth-library-oauth2-http" % "0.18.0" excludeAll excludIoGrpc
   val googleStorage: ModuleID = "com.google.apis" % "google-api-services-storage" % "v1-rev20250925-2.0.0" excludeAll excludIoGrpc // force this version
@@ -115,7 +115,7 @@ object Dependencies {
       excludeWorkbenchModel
     )
   val googleStorageLocal: ModuleID =
-    "com.google.cloud" % "google-cloud-nio" % "0.128.5" % "test" // needed for mocking google cloud storage. Should use same version as wb-libs
+    "com.google.cloud" % "google-cloud-nio" % "0.128.9" % "test" // needed for mocking google cloud storage. Should use same version as wb-libs
 
   val liquibaseCore: ModuleID = "org.liquibase" % "liquibase-core" % "4.33.0"
 
@@ -130,7 +130,7 @@ object Dependencies {
   val slf4jApi: ModuleID = "org.slf4j" % "slf4j-api" % slf4jVersion
   val slf4jSimple: ModuleID = "org.slf4j" % "slf4j-simple" % slf4jVersion
 
-  val okio: ModuleID = "com.squareup.okio" % "okio" % "3.16.0" excludeAll excludeWorkbenchUtil2
+  val okio: ModuleID = "com.squareup.okio" % "okio" % "3.16.4" excludeAll excludeWorkbenchUtil2
 
   // pact deps
   val pact4sV = "0.9.0"
@@ -188,7 +188,7 @@ object Dependencies {
   val terraCommonLib = tclExclusions("bio.terra" % "terra-common-lib" % tclVersion classifier "plain")
 
   // was included transitively before, now explicit
-  val commonsCodec: ModuleID = "commons-codec" % "commons-codec" % "1.19.0"
+  val commonsCodec: ModuleID = "commons-codec" % "commons-codec" % "1.20.0"
 
   val rootDependencies = Seq(
     // proactively pull in latest versions of Jackson libs, instead of relying on the versions

project/Settings.scala

@@ -68,7 +68,7 @@ object Settings {
   lazy val commonSettings =
     commonBuildSettings ++ commonAssemblySettings ++ commonTestSettings ++ List(
       organization := "org.broadinstitute.dsde.workbench",
-      scalaVersion := "2.13.17",
+      scalaVersion := "2.13.18",
       resolvers := proxyResolvers ++: resolvers.value ++: commonResolvers,
       scalacOptions ++= commonCompilerSettings,
       Compile / compile := (Compile / compile).dependsOn(Compile / scalafmtAll).value,

project/plugins.sbt

@@ -2,10 +2,10 @@ addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "2.3.1")
 
 addSbtPlugin("io.spray" % "sbt-revolver" % "0.10.0")
 
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.4.2")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "2.4.3")
 
-addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.5")
+addSbtPlugin("org.scalameta" % "sbt-scalafmt" % "2.5.6")
 
-addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.14.3")
+addSbtPlugin("ch.epfl.scala" % "sbt-scalafix" % "0.14.5")
 
 addDependencyTreePlugin