From c0be97c980b317061e6d6dda18895799e25e4c4b Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Mon, 26 Sep 2022 10:41:03 -0400
Subject: [PATCH] Cherry-pick required commits from cn_sprk_3.3.0_rebased.

---
 Dockerfile                       |  2 +-
 build.gradle                     | 21 ++++++---------------
 gatk                             |  5 +++--
 scripts/docker/dockertest.gradle |  2 +-
 4 files changed, 11 insertions(+), 19 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index b118b980c41..57f7f5ee5fb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -90,7 +90,7 @@ RUN echo "source activate gatk" > /root/run_unit_tests.sh && \
     echo "mkdir /gatk/srcdir" >> /root/run_unit_tests.sh && \
     echo "cp -rp /gatkCloneMountPoint/src/main/java/* /gatk/srcdir" >> /root/run_unit_tests.sh && \
     echo "export SOURCE_DIR=/gatk/srcdir" >> /root/run_unit_tests.sh && \
-    echo "export GRADLE_OPTS=\"-Xmx1024m -Dorg.gradle.daemon=false\"" >> /root/run_unit_tests.sh && \
+    echo "export GRADLE_OPTS=\"-Xmx1024m -Dorg.gradle.daemon=false --add-opens java.prefs/java.util.prefs=ALL-UNNAMED\"" >> /root/run_unit_tests.sh && \
     echo "export CP_DIR=/gatk/testClasses" >> /root/run_unit_tests.sh && \
     echo "ln -s /gatkCloneMountPoint/src/ /gatkCloneMountPoint/scripts/docker/src" >> /root/run_unit_tests.sh && \
     echo "ln -s /gatkCloneMountPoint/build/ /gatkCloneMountPoint/scripts/docker/build" >> /root/run_unit_tests.sh && \
diff --git a/build.gradle b/build.gradle
index 2df5ff082ca..a22bac75e66 100644
--- a/build.gradle
+++ b/build.gradle
@@ -23,8 +23,6 @@ import com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar
 import de.undercouch.gradle.tasks.download.Download
 
 import javax.tools.ToolProvider
-import java.time.format.DateTimeFormatter
-import java.time.ZonedDateTime
 
 mainClassName = "org.broadinstitute.hellbender.Main"
 
@@ -138,21 +136,13 @@ def looksLikeWereInAGitRepository(){
 // Ensure that we have a clone of the git repository, and resolve any required git-lfs
 // resource files that are needed to run the build but are still lfs stub files.
 def ensureBuildPrerequisites(largeResourcesFolder, buildPrerequisitesMessage, skipGitCheck) {
-    if (!JavaVersion.current().isJava8Compatible()) {
-        throw new GradleException(
-                "Java 17 or later is required to build GATK, but ${JavaVersion.current()} was found. "
-                        + "$buildPrerequisitesMessage")
+    if (!JavaVersion.current().equals(JavaVersion.VERSION_17)) {
+        println("Warning: using Java ${JavaVersion.current()} but only Java 17 has been tested.")
     }
-    //TODO: fix this comment
-    // Make sure we can get a ToolProvider class loader (for Java 8). If not we may have just a JRE.
-    if (JavaVersion.current().isJava8() && ToolProvider.getSystemToolClassLoader() == null) {
+    if (!JavaVersion.current().isCompatibleWith(JavaVersion.VERSION_17)) {
         throw new GradleException(
-                "The ClassLoader obtained from the Java ToolProvider is null. "
-                + "A full Java 17 JDK must be installed, check that you are not using a JRE. $buildPrerequisitesMessage")
-    }
-    //TODO: fix this - the gradle version we're using has no isJava17
-    if (!JavaVersion.current().isJava8() && !JavaVersion.current().isJava11()) {
-        println("Warning: using Java ${JavaVersion.current()} but only Java 17 has been tested.")
+                "A Java 17 compatible (Java 17 or later) version is required to build GATK, but ${JavaVersion.current()} was found. "
+                        + "$buildPrerequisitesMessage")
     }
     if (!skipGitCheck && !looksLikeWereInAGitRepository() ) {
         throw new GradleException("This doesn't appear to be a git folder. " +
@@ -615,6 +605,7 @@ task shadowTestClassJar(type: ShadowJar){
 
 // A minimal jar that only contains the extra dependencies needed for running the tests
 task shadowTestJar(type: ShadowJar){
+    dependsOn 'compileTestUtilsJava', 'processTestUtilsResources'
     group = "Shadow"
     description = " A minimal jar that only contains the extra dependencies needed for running the tests that arent packaged in the main shadow jar"
     from {
diff --git a/gatk b/gatk
index 67894569771..ded0e626559 100755
--- a/gatk
+++ b/gatk
@@ -148,8 +148,9 @@ PACKAGED_LOCAL_JAR_OPTIONS= [
                     "--add-opens", "java.base/jdk.internal.module=ALL-UNNAMED",
                     "--add-opens", "java.base/java.lang.module=ALL-UNNAMED",
                     "--add-opens", "java.security.jgss/sun.security.krb5=ALL-UNNAMED",                                                                                                                                                                                                                                                                           "-Dio.netty.tryReflectionSetAccessible=true"
-                    "--add-opens", "java.prefs/java.util.prefs=ALL-UNNAMED"
-    ]
+                    "--add-opens", "java.prefs/java.util.prefs=ALL-UNNAMED",
+                    "-Dio.netty.tryReflectionSetAccessible=true"
+]
 
 DEFAULT_SPARK_ARGS_PREFIX = '--conf'
 DEFAULT_SPARK_ARGS = {
diff --git a/scripts/docker/dockertest.gradle b/scripts/docker/dockertest.gradle
index 5438a1d81ed..bf21192493f 100644
--- a/scripts/docker/dockertest.gradle
+++ b/scripts/docker/dockertest.gradle
@@ -238,7 +238,7 @@ task testOnPackagedReleaseJar(type: Test){
             '-Dio.netty.tryReflectionSetAccessible=true'
     ]
 
-    classpath = files( testClassesJar, testDependencyJar, gatkJar )
+    classpath = files( gatkJar, testClassesJar, testDependencyJar)
     testClassesDirs = files(testClassesUnpacked)
 }