Revert "Revert "WX-1409 Java 17 (#7342)" (#7343)"

This reverts commit 227778a.

.github/set_up_cromwell_action/action.yml

@@ -3,7 +3,8 @@
 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:
@@ -12,13 +13,13 @@ runs:
       #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  
+      - 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: adopt@1.11
+        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: adopt@1.11
+          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

@@ -104,6 +104,14 @@ jobs:
         set -e
         echo Running test.sh
         ./src/ci/bin/test.sh
+    # If a build step fails, activate SSH and idle for 60 minutes
+    # - name: Setup tmate session
+    #  if: ${{ failure() }}
+    #  uses: mxschmitt/action-tmate@v3
+    #  timeout-minutes: 60
+    #  with:
+    #    limit-access-to-actor: true
+    #    detached: true
     # always() is some github magic that forces the following step to run, even when the previous fails.
     # Without it, the if statement won't be evaluated on a test failure.
     - uses: ravsamhq/notify-slack-action@v2

.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: adopt@1.11
+          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

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Cromwell Change Log
 
+## 87 Release Notes
+
+### Java 17
+
+As of this version, a distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and
+containerized using [Eclipse Temurin](https://adoptium.net/temurin/releases/?version=17).
+
 ## 86 Release Notes
 
 ### GCP Batch

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/Releases.md

@@ -19,8 +19,8 @@ Mac users with Homebrew can also get Cromwell with the command `brew install cro
 This documentation frequently refers to a "Cromwell jar" with a name like `cromwell-<version>.jar`. 
 This is the main artifact in Cromwell releases that contains all executable Cromwell code and default configuration.   
 
-A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
-[AdoptOpenJDK 11 HotSpot](https://adoptopenjdk.net/).
+A distribution of Java 17 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 17 HotSpot](https://adoptopenjdk.net/).
 
 For users running a Cromwell server [a docker image](https://hub.docker.com/r/broadinstitute/cromwell) has been made available.
 

docs/tutorials/FiveMinuteIntro.md

@@ -3,11 +3,11 @@
 ### Prerequisites:
 
 * A Unix-based operating system (yes, that includes Mac!)
-* A Java 11 runtime environment 
+* A Java 17 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)
-      * `sdk install java 11.0.16-tem` as of the time of this writing
+    * We recommend [SDKMAN](https://sdkman.io/install) to install the latest 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
+      * `sdk install 17.0.9-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

@@ -63,7 +63,7 @@ object Publishing {
       val additionalDockerInstr: Seq[Instruction] = (dockerCustomSettings ?? Nil).value
 
       new Dockerfile {
-        from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
+        from("us.gcr.io/broad-dsp-gcr-public/base/jre:17-debian")
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
@@ -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>