WX-1409 Java 17

.github/set_up_cromwell_action/action.yml

@@ -3,22 +3,23 @@
 name: 'Set Up Cromwell Steps'
 description: Specific steps that will set up git secrets, java, sbt, and Cromwell on the local machine. 
 inputs:
-  cromwell_repo_token: #As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell.
+  cromwell_repo_token:
+    description: "As an input to this action, you are required to pass in a token that can be used to authenticate while checking out Cromwell."
     required: true
 
 runs:
   using: "composite" # <-- this allows these steps to be used by other workflows.
   steps:
       #Allows this github action to use a cache to store stuff like Java and sbt files between runs.
-      - uses: actions/checkout@v3
-        name: Checkout Coursier Cache
-      - uses: coursier/cache-action@v6  
-        name: Enable Coursier Cache
+      # - uses: actions/checkout@v3
+      #   name: Checkout Coursier Cache
+      # - uses: coursier/cache-action@v6
+      #   name: Enable Coursier Cache
 
       #Cromwell requires git-secrets be setup. Here, we set up secrets and verify success with a script.
       - name: Git secrets setup 
         run: |
-          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
+          git clone --quiet https://github.com/awslabs/git-secrets.git ~/git-secrets
           cd ~/git-secrets
           git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
           sudo make install
@@ -43,5 +44,4 @@ runs:
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 11
-
+          java-version: 17

.github/workflows/chart_update_on_merge.yml

@@ -23,9 +23,10 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: olafurpg/setup-scala@v10
+    - uses: actions/setup-java@v4
       with:
-        java-version: [email protected]
+        distribution: 'temurin'
+        java-version: '17'
     - name: Clone Cromwhelm
       uses: actions/checkout@v2
       with:

.github/workflows/docker_build_test.yml

@@ -25,9 +25,10 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
-      - uses: olafurpg/setup-scala@v10
+      - uses: actions/setup-java@v4
         with:
-          java-version: [email protected]
+          distribution: 'temurin'
+          java-version: '17'
       # The following invocation should be as similar as possible to the one in chart_update_on_merge.yml
       # To state the obvious: This test should not publish anything. It should simply verify that the build completes.
       - name: Build Cromwell Docker

.github/workflows/integration_tests.yml

@@ -90,6 +90,12 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 120
     steps:
+    # - name: Setup tmate session
+    #  uses: mxschmitt/action-tmate@v3
+    #  timeout-minutes: 10
+    #  with:
+    #    limit-access-to-actor: true
+    #    detached: true
     - uses: actions/checkout@v3 # checkout the cromwell repo
       with:
         ref: ${{ inputs.target-branch }}

.github/workflows/trivy.yml

@@ -20,9 +20,10 @@ jobs:
       - uses: actions/checkout@v2
 
       # fetch SBT package
-      - uses: olafurpg/setup-scala@v10
+      - uses: actions/setup-java@v4
         with:
-          java-version: [email protected]
+          distribution: 'temurin'
+          java-version: '17'
 
       # set up SBT cache
       - uses: actions/cache@v2

.sdkmanrc

@@ -1,3 +1,3 @@
 # Enable auto-env through the sdkman_auto_env config
 # Add key=value pairs of SDKs to use below
-java=11.0.11.hs-adpt
+java=17.0.9-tem

centaur/src/main/scala/centaur/api/DaemonizedDefaultThreadFactory.scala

@@ -14,8 +14,7 @@ import java.util.concurrent.atomic.AtomicInteger
   * > main thread).
   */
 object DaemonizedDefaultThreadFactory extends ThreadFactory {
-  private val s = System.getSecurityManager
-  private val group = if (s != null) s.getThreadGroup else Thread.currentThread.getThreadGroup
+  private val group = Thread.currentThread.getThreadGroup
   private val threadNumber = new AtomicInteger(1)
   private val namePrefix = "daemonpool-thread-"
 

cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/CloudNioPath.scala

@@ -176,7 +176,7 @@ class CloudNioPath(filesystem: CloudNioFileSystem, private[spi] val unixPath: Un
   ): WatchKey = throw new UnsupportedOperationException
 
   override def iterator(): java.util.Iterator[Path] =
-    if (unixPath.isEmpty || unixPath.isRoot) {
+    if (unixPath.izEmpty || unixPath.isRoot) {
       java.util.Collections.emptyIterator()
     } else {
       unixPath.split().to(LazyList).map(part => newPath(UnixPath.getPath(part)).asInstanceOf[Path]).iterator.asJava

cloud-nio/cloud-nio-spi/src/main/scala/cloud/nio/spi/UnixPath.scala

@@ -67,7 +67,7 @@ final private[spi] case class UnixPath(path: String) extends CharSequence {
 
   def isAbsolute: Boolean = UnixPath.isAbsolute(path)
 
-  def isEmpty: Boolean = path.isEmpty
+  def izEmpty: Boolean = path.isEmpty
 
   def hasTrailingSeparator: Boolean = UnixPath.hasTrailingSeparator(path)
 

docs/Configuring.md

@@ -689,7 +689,7 @@ This limit may be configured via the configuration value:
 
 ```hocon
 yaml {
-  max-depth = 1000
+  max-depth = 100
 }
 ```
 

docs/tutorials/FiveMinuteIntro.md

@@ -6,7 +6,7 @@
 * A Java 11 runtime environment 
     * You can see what you have by running `$ java -version` on a terminal.
     * If not, consider installing via conda or brew [as explained here](../Releases.md).
-    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 11 build of [Temurin](https://adoptium.net/temurin/releases/?version=11)
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
       * `sdk install java 11.0.16-tem` as of the time of this writing
     * You might need to update the `export JAVA_HOME` in your bash profile to point to your JAVA install location.
 * A sense of adventure!

project/Publishing.scala

@@ -163,8 +163,7 @@ object Publishing {
   val additionalResolvers = List(
     broadArtifactoryResolver,
     broadArtifactoryResolverSnap,
-    Resolver.sonatypeRepo("releases")
-  )
+  ) ++ Resolver.sonatypeOssRepos("releases")
 
   private val artifactoryCredentialsFile =
     file("target/ci/resources/artifactory_credentials.properties").getAbsoluteFile

publish/docker-setup.sh

@@ -20,7 +20,7 @@ mkdir -p /etc/apt/keyrings
 wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
 echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^VERSION_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 apt update
-apt install -y temurin-11-jdk
+apt install -y temurin-17-jdk
 
 # Install jq 1.6 to ensure --rawfile is supported
 curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /usr/bin/jq

runConfigurations/renderCiResources.run.xml

@@ -7,8 +7,8 @@
     </option>
     <option name="tasks" value="renderCiResources" />
     <option name="useSbtShell" value="false" />
-    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M -XX:+CMSClassUnloadingEnabled" />
+    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M" />
     <option name="workingDir" value="$PROJECT_DIR$" />
     <method v="2" />
   </configuration>
-</component>
+</component>

src/ci/bin/test.inc.sh

@@ -746,7 +746,7 @@ cromwell::private::login_docker() {
 
 cromwell::private::render_secure_resources() {
     # Avoid docker output to sbt's stderr by pulling the image here
-    docker pull broadinstitute/dsde-toolbox:dev | cat
+    docker pull --quiet broadinstitute/dsde-toolbox:dev | cat
     # Copy the CI resources, then render the secure resources using Vault
     sbt -Dsbt.supershell=false --warn renderCiResources \
     || if [[ "${CROMWELL_BUILD_IS_CI}" == "true" ]]; then

src/ci/docker-compose/cromwell-test/Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:focal
+FROM ubuntu:latest
 
 WORKDIR /cromwell-test/
 COPY docker-setup.sh ./

src/ci/docker-compose/cromwell-test/docker-setup.sh

@@ -25,13 +25,11 @@ apt-get install -y \
     sudo \
     wget \
 
-# setup install for adoptopenjdk
-# https://adoptopenjdk.net/installation.html#linux-pkg-deb
-wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public | apt-key add -
-echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
-        grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
-    ) main" |
-    tee /etc/apt/sources.list.d/adoptopenjdk.list
+# setup install for Temurin
+# https://adoptium.net/installation/linux/
+mkdir -p /etc/apt/keyrings
+wget -O - https://packages.adoptium.net/artifactory/api/gpg/key/public | tee /etc/apt/keyrings/adoptium.asc
+echo "deb [signed-by=/etc/apt/keyrings/adoptium.asc] https://packages.adoptium.net/artifactory/deb $(awk -F= '/^UBUNTU_CODENAME/{print$2}' /etc/os-release) main" | tee /etc/apt/sources.list.d/adoptium.list
 
 # setup install for gcloud
 # https://cloud.google.com/sdk/docs/install#deb
@@ -52,7 +50,7 @@ add-apt-repository \
 # install packages that required setup
 apt-get update
 apt-get install -y \
-    adoptopenjdk-11-hotspot \
+    temurin-17-jdk \
     containerd.io \
     docker-ce \
     docker-ce-cli \