update to jdk 11 [AS-594]

.github/workflows/test.yml

@@ -35,10 +35,10 @@ jobs:
       - name: coursier-cache-action
         uses: coursier/cache-action@v5
 
-      - name: Set up JDK 1.8
+      - name: Set up JDK 11
         uses: actions/setup-java@v1
         with:
-          java-version: 1.8
+          java-version: 11
 
       - name: Git secrets setup
         run: |

.java-version

@@ -1 +1 @@
-1.8
+11

Dockerfile

@@ -1,4 +1,4 @@
-FROM us.gcr.io/broad-dsp-gcr-public/base/jre:8-debian
+FROM us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian
 
 # To run, must build the jar using ./docker/build.sh
 

automation/Dockerfile-tests

@@ -1,4 +1,4 @@
-FROM bigtruedata/sbt
+FROM broadinstitute/scala-baseimage:jdk11-2.12.12-1.4.7
 
 COPY src /app/src
 COPY minnie-kenny.sh /app

automation/project/Settings.scala

@@ -15,7 +15,7 @@ object Settings {
   //coreDefaultSettings + defaultConfigs = the now deprecated defaultSettings
   val commonBuildSettings = Defaults.coreDefaultSettings ++ Defaults.defaultConfigs ++ Seq(
     javaOptions += "-Xmx2G",
-    javacOptions ++= Seq("-source", "1.8", "-target", "1.8"),
+    javacOptions ++= Seq("--release", "11"),
     addCompilerPlugin(scalafixSemanticdb)
   )
 
@@ -24,7 +24,6 @@ object Settings {
     "-deprecation",
     "-feature",
     "-encoding", "utf8",
-    "-target:jvm-1.8",
     "-Xmax-classfile-name", "100"
   )
 

automation/project/build.properties

@@ -1 +1 @@
-sbt.version = 1.4.6
+sbt.version = 1.4.7

core/src/test/scala/org/broadinstitute/dsde/rawls/RawlsTestUtils.scala

@@ -3,7 +3,7 @@ package org.broadinstitute.dsde.rawls
 import akka.http.scaladsl.model.{StatusCode, StatusCodes}
 import org.broadinstitute.dsde.rawls.dataaccess.slick.TestDriverComponent
 import org.broadinstitute.dsde.rawls.model.Workspace
-import org.mockserver.model.StringBody
+import org.mockserver.model.RegexBody
 import org.scalatest.exceptions.TestFailedException
 import org.scalatest.Suite
 
@@ -71,8 +71,8 @@ trait RawlsTestUtils extends Suite with TestDriverComponent with Matchers {
   }
 
   // MockServer's .withBody doesn't have a built-in string contains feature.  This serves that purpose.
-  def mockServerContains(text: String): StringBody = {
-    val anythingWithNewlines = "((.|\n|\r)*)"
-    StringBody.regex(anythingWithNewlines + Regex.quote(text.toString) + anythingWithNewlines)
+  def mockServerContains(text: String): RegexBody = {
+    // "(?s)" turns on DOTALL mode, where a "." matches a line break as well as any character
+    new RegexBody("(?s).*" + Regex.quote(text) + ".*")
   }
 }

docker/build.sh

@@ -108,7 +108,7 @@ function make_jar()
     if [ "$SKIP_TESTS" != "skip-tests" ]; then
         DOCKER_RUN="$DOCKER_RUN --link mysql:mysql"
     fi
-    DOCKER_RUN="$DOCKER_RUN -e SKIP_TESTS=$SKIP_TESTS -e GIT_MODEL_HASH=$GIT_MODEL_HASH -e GIT_COMMIT -e BUILD_NUMBER -v $PWD:/working -v sbt-cache:/root/.sbt -v jar-cache:/root/.ivy2 -v coursier-cache:/root/.cache/coursier broadinstitute/scala-baseimage /working/docker/install.sh /working"
+    DOCKER_RUN="$DOCKER_RUN -e SKIP_TESTS=$SKIP_TESTS -e GIT_MODEL_HASH=$GIT_MODEL_HASH -e GIT_COMMIT -e BUILD_NUMBER -v $PWD:/working -v sbt-cache:/root/.sbt -v jar-cache:/root/.ivy2 -v coursier-cache:/root/.cache/coursier broadinstitute/scala-baseimage:jdk11-2.12.11-1.4.7 /working/docker/install.sh /working"
     JAR_CMD=$($DOCKER_RUN 1>&2)
     EXIT_CODE=$?
 
@@ -130,7 +130,7 @@ function artifactory_push()
     ARTIFACTORY_USERNAME=dsdejenkins
     ARTIFACTORY_PASSWORD=$(docker run -e VAULT_TOKEN=$VAULT_TOKEN broadinstitute/dsde-toolbox vault read -field=password secret/dsp/accts/artifactory/dsdejenkins)
     echo "Publishing to artifactory..."
-    docker run --rm -v $PWD:/$PROJECT -v sbt-cache:/root/.sbt -v jar-cache:/root/.ivy2 -v coursier-cache:/root/.cache/coursier -w="/$PROJECT" -e ARTIFACTORY_USERNAME=$ARTIFACTORY_USERNAME -e ARTIFACTORY_PASSWORD=$ARTIFACTORY_PASSWORD broadinstitute/scala-baseimage:scala-2.11.8 /$PROJECT/core/src/bin/publishSnapshot.sh
+    docker run --rm -v $PWD:/$PROJECT -v sbt-cache:/root/.sbt -v jar-cache:/root/.ivy2 -v coursier-cache:/root/.cache/coursier -w="/$PROJECT" -e ARTIFACTORY_USERNAME=$ARTIFACTORY_USERNAME -e ARTIFACTORY_PASSWORD=$ARTIFACTORY_PASSWORD broadinstitute/scala-baseimage:jdk11-2.12.11-1.4.7 /$PROJECT/core/src/bin/publishSnapshot.sh
 }
 
 function docker_cmd()

docker/install.sh

@@ -16,7 +16,7 @@ if [ "$SKIP_TESTS" = "skip-tests" ]; then
 	echo skipping tests
 else
   echo "starting sbt test ..."
-	sbt -J-Xms5g -J-Xmx5g -J-XX:MaxMetaspaceSize=5g test -Dmysql.host=mysql -Dmysql.port=3306
+	sbt -J-Xms5g -J-Xmx5g -J-XX:MaxMetaspaceSize=5g test -Dmysql.host=mysql -Dmysql.port=3306 -Dsecrets.skip=true
 	echo "sbt test done"
 fi
 

project/Dependencies.scala

@@ -87,7 +87,7 @@ object Dependencies {
   val scalaUri: ModuleID =        "io.lemonlabs"                  %% "scala-uri"            % "3.0.0"
   val scalatest: ModuleID =       "org.scalatest"                 %% "scalatest"            % "3.2.2" % "test"
   val mockito: ModuleID =         "org.scalatestplus"             %% "mockito-3-4"          % "3.2.2.0" % Test
-  val mockserverNetty: ModuleID = "org.mock-server"               % "mockserver-netty"      % "3.9.2" % "test"
+  val mockserverNetty: ModuleID = "org.mock-server"               % "mockserver-netty"      % "5.11.2" % "test"
   val ficus: ModuleID =           "com.iheart"                    %% "ficus"                % "1.4.0"
   val scalaCache: ModuleID =      "com.github.cb372"              %% "scalacache-caffeine"  % "0.24.2"
   val apacheCommonsIO: ModuleID = "commons-io"                    % "commons-io"            % "2.6"

project/Merging.scala

@@ -9,6 +9,7 @@ object Merging {
     case PathList("com", "typesafe", _ @ _*) => MergeStrategy.last
     case PathList("com", "google", "auto", "value", _ @ _*) => MergeStrategy.last
     case PathList("io", "sundr", _ @ _*) => MergeStrategy.last
+    case PathList("javax", "activation", _ @ _*) => MergeStrategy.first
     // For the following error:
     //[error] java.lang.RuntimeException: deduplicate: different file contents found in the following:
     //[error] /root/.cache/coursier/v1/https/repo1.maven.org/maven2/com/google/protobuf/protobuf-java/3.11.4/protobuf-java-3.11.4.jar:google/protobuf/field_mask.proto

project/Settings.scala

@@ -27,6 +27,10 @@ object Settings {
     javaOptions += "-Xmx2G"
   )
 
+  val java11BuildSettings = Seq( // can be wrapped into commonBuildSettings when rawls-model can publish java 11
+    javacOptions ++= Seq("--release", "11")
+  )
+
   val commonCompilerSettings = Seq(
     "-unchecked",
     "-feature",
@@ -78,13 +82,14 @@ object Settings {
   val googleSettings = commonSettings ++ List(
     name := "workbench-google",
     libraryDependencies ++= googleDependencies
-  ) ++ versionSettings ++ noPublishSettings
+  ) ++ versionSettings ++ noPublishSettings ++ java11BuildSettings
 
   //the full list of settings for the rawlsModel project (see build.sbt)
   //coreDefaultSettings (inside commonSettings) sets the project name, which we want to override, so ordering is important.
   //thus commonSettings needs to be added first.
   val modelSettings = cross212and213 ++ commonSettings ++ List(
     name := "rawls-model",
+    javacOptions ++= Seq("--release", "8"), // has to publish a java 8 artifact
     libraryDependencies ++= modelDependencies
   ) ++ versionSettings ++ publishSettings
 
@@ -94,15 +99,15 @@ object Settings {
   val utilSettings = commonSettings ++ List(
     name := "workbench-util",
     libraryDependencies ++= utilDependencies
-  ) ++ versionSettings ++ noPublishSettings
+  ) ++ versionSettings ++ noPublishSettings ++ java11BuildSettings
 
   //the full list of settings for the workbenchMetrics project (see build.sbt)
   //coreDefaultSettings (inside commonSettings) sets the project name, which we want to override, so ordering is important.
   //thus commonSettings needs to be added first.
   val metricsSettings = commonSettings ++ List(
     name := "workbench-metrics",
     libraryDependencies ++= metricsDependencies
-  ) ++ versionSettings ++ noPublishSettings
+  ) ++ versionSettings ++ noPublishSettings ++ java11BuildSettings
 
   //the full list of settings for the rawlsCore project (see build.sbt)
   //coreDefaultSettings (inside commonSettings) sets the project name, which we want to override, so ordering is important.
@@ -111,7 +116,7 @@ object Settings {
     name := "rawls-core",
     version := "0.1",
     libraryDependencies ++= rawlsCoreDependencies
-  ) ++ antlr4CodeGenerationSettings ++ rawlsAssemblySettings ++ noPublishSettings ++ rawlsCompileSettings
+  ) ++ antlr4CodeGenerationSettings ++ rawlsAssemblySettings ++ noPublishSettings ++ rawlsCompileSettings ++ java11BuildSettings
   //NOTE: rawlsCoreCompileSettings above has to be last, because something in commonSettings or rawlsAssemblySettings
   //overwrites it if it's before them. I (hussein) don't know what that is and I don't care to poke the bear to find out.
 
@@ -121,6 +126,6 @@ object Settings {
   val rootSettings = commonSettings ++ List(
     name := "rawls",
     version := "0.1"
-  ) ++ rawlsAssemblySettings ++ noPublishSettings ++ rawlsCompileSettings
+  ) ++ rawlsAssemblySettings ++ noPublishSettings ++ rawlsCompileSettings ++ java11BuildSettings
   //See immediately above NOTE.
 }

project/Testing.scala

@@ -1,3 +1,4 @@
+import MinnieKenny.testSettings
 import sbt.Keys._
 import sbt._
 
@@ -22,6 +23,9 @@ object Testing {
 
   val commonTestSettings: Seq[Setting[_]] = List(
 
+    testOptions in Test += Tests.Setup(() =>
+      sys.props += "mockserver.logLevel" -> "WARN"
+    ),
     // SLF4J initializes itself upon the first logging call.  Because sbt
     // runs tests in parallel it is likely that a second thread will
     // invoke a second logging call before SLF4J has completed
@@ -55,7 +59,7 @@ object Testing {
     (testOnly in Test) := ((testOnly in Test) dependsOn validMySqlHost).evaluated,
 
     parallelExecution in Test := false
-  ) ++ MinnieKenny.testSettings
+  ) ++ (if (sys.props.getOrElse("secrets.skip", false) != "true") MinnieKenny.testSettings else List())
 
   implicit class ProjectTestSettings(val project: Project) extends AnyVal {
     def withTestSettings: Project = project

project/build.properties

@@ -1 +1 @@
-sbt.version=1.4.6
+sbt.version=1.4.7