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

This reverts commit 0ecbf53.

.github/set_up_cromwell_action/action.yml

@@ -3,8 +3,7 @@
 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:
-    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."
+  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.
     required: true
 
 runs:
@@ -13,13 +12,13 @@ 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 --quiet https://github.com/awslabs/git-secrets.git ~/git-secrets
+          git clone https://github.com/awslabs/git-secrets.git ~/git-secrets
           cd ~/git-secrets
           git checkout ad82d68ee924906a0401dfd48de5057731a9bc84
           sudo make install
@@ -44,4 +43,5 @@ runs:
         uses: actions/setup-java@v3
         with:
           distribution: temurin
-          java-version: 17
+          java-version: 11
+

.github/workflows/chart_update_on_merge.yml

@@ -23,10 +23,9 @@ jobs:
         repository: broadinstitute/cromwell
         token: ${{ secrets.BROADBOT_GITHUB_TOKEN }} # Has to be set at checkout AND later when pushing to work
         path: cromwell
-    - uses: actions/setup-java@v4
+    - uses: olafurpg/setup-scala@v10
       with:
-        distribution: 'temurin'
-        java-version: '17'
+        java-version: adopt@1.11
     - name: Clone Cromwhelm
       uses: actions/checkout@v2
       with:

.github/workflows/docker_build_test.yml

@@ -25,10 +25,9 @@ jobs:
           repository: broadinstitute/cromwell
           token: ${{ secrets.BROADBOT_GITHUB_TOKEN }}
           path: cromwell
-      - uses: actions/setup-java@v4
+      - uses: olafurpg/setup-scala@v10
         with:
-          distribution: 'temurin'
-          java-version: '17'
+          java-version: adopt@1.11
       # 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

@@ -104,14 +104,6 @@ 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

@@ -20,10 +20,9 @@ jobs:
       - uses: actions/checkout@v2
 
       # fetch SBT package
-      - uses: actions/setup-java@v4
+      - uses: olafurpg/setup-scala@v10
         with:
-          distribution: 'temurin'
-          java-version: '17'
+          java-version: adopt@1.11
 
       # 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=17.0.9-tem
+java=11.0.11.hs-adpt

CHANGELOG.md

@@ -1,12 +1,5 @@
 # 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

@@ -14,7 +14,8 @@ import java.util.concurrent.atomic.AtomicInteger
   * > main thread).
   */
 object DaemonizedDefaultThreadFactory extends ThreadFactory {
-  private val group = Thread.currentThread.getThreadGroup
+  private val s = System.getSecurityManager
+  private val group = if (s != null) s.getThreadGroup else 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.izEmpty || unixPath.isRoot) {
+    if (unixPath.isEmpty || 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 izEmpty: Boolean = path.isEmpty
+  def isEmpty: 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 = 100
+  max-depth = 1000
 }
 ```
 

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 17 is required to run Cromwell. Cromwell is developed, tested, and containerized using
-[AdoptOpenJDK 17 HotSpot](https://adoptopenjdk.net/).
+A distribution of Java 11 is required to run Cromwell. Cromwell is developed, tested, and containerized using
+[AdoptOpenJDK 11 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 17 runtime environment 
+* 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 17 build of [Temurin](https://adoptium.net/temurin/releases/?version=17)
-      * `sdk install 17.0.9-tem` as of the time of this writing
+    * 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
     * 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:17-debian")
+        from("us.gcr.io/broad-dsp-gcr-public/base/jre:11-debian")
         expose(8000)
         add(artifact, artifactTargetPath)
         runRaw(s"ln -s $artifactTargetPath /app/$projectName.jar")
@@ -163,7 +163,8 @@ object Publishing {
   val additionalResolvers = List(
     broadArtifactoryResolver,
     broadArtifactoryResolverSnap,
-  ) ++ Resolver.sonatypeOssRepos("releases")
+    Resolver.sonatypeRepo("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-17-jdk
+apt install -y temurin-11-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" />
+    <option name="vmparams" value="-Xms512M -Xmx1024M -Xss1M -XX:+CMSClassUnloadingEnabled" />
     <option name="workingDir" value="$PROJECT_DIR$" />
     <method v="2" />
   </configuration>
-</component>
+</component>

scripts/docker-compose-mysql/README.md

@@ -0,0 +1 @@
+Looking for the MySQL docs? Checkout the [Cromwell documentation](https://cromwell.readthedocs.io/en/develop/Configuring/#database)!

scripts/docker-compose-mysql/compose/cromwell/Dockerfile

@@ -0,0 +1,9 @@
+FROM broadinstitute/cromwell:develop
+
+RUN git clone https://github.com/vishnubob/wait-for-it.git
+RUN mkdir cromwell-working-dir
+WORKDIR cromwell-working-dir
+
+COPY ./app-config /app-config
+
+ENTRYPOINT ["/bin/sh", "-c"]

scripts/docker-compose-mysql/compose/cromwell/app-config/cromwell-application.conf

@@ -0,0 +1,61 @@
+include required(classpath("application"))
+
+# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
+# https://github.com/broadinstitute/cromwell/issues
+
+call-caching {
+  enabled = false
+}
+
+backend {
+  default = "Local"
+  providers {
+    Local {
+      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
+      config {
+        run-in-background = true
+        runtime-attributes = "String? docker Int? max_runtime = 2"
+        submit = "/bin/bash ${script}"
+        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"
+
+        # Root directory where Cromwell writes job results. This directory must be
+        # visible and writeable by the Cromwell process as well as the jobs that Cromwell
+        # launches.
+        root: "cromwell-executions"
+
+        filesystems {
+          local {
+            localization: [
+              "soft-link", "hard-link", "copy"
+            ]
+
+            caching {
+              duplication-strategy: [
+                "soft-link"
+              ]
+
+              # Possible values: file, path
+              # "file" will compute an md5 hash of the file content.
+              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
+              # in order to allow for the original file path to be hashed.
+              hashing-strategy: "path"
+
+              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
+              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
+              check-sibling-md5: false
+            }
+          }
+        }
+      }
+    }
+  }
+}
+
+database {
+  db.url = "jdbc:mysql://mysql-db/cromwell_db?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true"
+  db.user = "cromwell"
+  db.password = "cromwell"
+  db.driver = "com.mysql.cj.jdbc.Driver"
+  profile = "slick.jdbc.MySQLProfile$"
+  db.connectionTimeout = 15000
+}

scripts/docker-compose-mysql/compose/mysql/init/init_user.sql

@@ -0,0 +1,4 @@
+CREATE USER 'cromwell'@'localhost' IDENTIFIED BY 'cromwell';
+GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'localhost' WITH GRANT OPTION;
+CREATE USER 'cromwell'@'%' IDENTIFIED BY 'cromwell';
+GRANT ALL PRIVILEGES ON cromwell_db.* TO 'cromwell'@'%' WITH GRANT OPTION;

scripts/docker-compose-mysql/docker-compose.yml

@@ -0,0 +1,22 @@
+version: '2'
+services:
+  cromwell:
+    build: 
+      context: ./compose/cromwell
+    volumes:
+      - ./cromwell-executions:/cromwell-working-dir/cromwell-executions
+    command: ["/wait-for-it/wait-for-it.sh mysql-db:3306 -t 120 -- java -Dconfig.file=/app-config/cromwell-application.conf -jar /app/cromwell.jar server"]
+    links:
+      - mysql-db
+    ports:
+      - "80:8000"
+  mysql-db:
+    image: "mysql:5.7"
+    environment:
+      - MYSQL_ROOT_PASSWORD=cromwell
+      - MYSQL_DATABASE=cromwell_db
+    volumes:
+      - ./compose/mysql/init:/docker-entrypoint-initdb.d
+      - ./compose/mysql/data:/var/lib/mysql
+    ports:
+      - "3307:3306"

scripts/docker-compose-mysql/jes-cromwell/docker-compose.yml

@@ -0,0 +1,9 @@
+version: '2'
+services:
+  cromwell:
+    volumes:
+      - $HOME/.config/gcloud:/root/.config/gcloud
+      - ./jes-cromwell/jes-config:/app-config
+    environment:
+      - GOOGLE_APPLICATION_CREDENTIALS=/root/.config/gcloud/application_default_credentials.json
+

scripts/docker-compose-mysql/jes-cromwell/jes-config/application.conf

@@ -0,0 +1,73 @@
+include required(classpath("application"))
+
+# Note: If you spot a mistake in this configuration sample, please let us know by making an issue at:
+# https://github.com/broadinstitute/cromwell/issues
+
+system.new-workflow-poll-rate=1
+
+google {
+
+  application-name = "cromwell"
+
+  auths = [
+    {
+      name = "application-default"
+      scheme = "application_default"
+    }
+  ]
+}
+
+engine {
+  filesystems {
+     gcs {
+       auth = "application-default"
+     }
+  }
+}
+
+call-caching {
+  enabled = false
+}
+
+backend {
+  default = "Jes"
+  providers {
+    Jes {
+          actor-factory = "cromwell.backend.impl.jes.JesBackendLifecycleActorFactory"
+          config {
+            // Google project
+            project = "broad-dsde-cromwell-dev"
+
+            // Base bucket for workflow executions
+            root = "gs://tjeandet-cromwell-execs"
+
+            // Polling for completion backs-off gradually for slower-running jobs.
+            // This is the maximum polling interval (in seconds):
+            maximum-polling-interval = 600
+
+            genomics {
+              // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
+              // Pipelines and manipulate auth JSONs.
+              auth = "application-default"
+              // Endpoint for APIs, no reason to change this unless directed by Google.
+              endpoint-url = "https://genomics.googleapis.com/"
+            }
+
+            filesystems {
+              gcs {
+                // A reference to a potentially different auth for manipulating files via engine functions.
+                auth = "application-default"
+              }
+            }
+          }
+    }
+  }
+}
+
+database {
+  db.url = "jdbc:mysql://mysql-db/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
+  db.user = "cromwell"
+  db.password = "cromwell"
+  db.driver = "com.mysql.cj.jdbc.Driver"
+  profile = "slick.jdbc.MySQLProfile$"
+}