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Move the --add-opens directives to the jar file.
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@cmnbroad
cmnbroad committed Nov 7, 2022
1 parent 0da86ff commit df452ef
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Showing 3 changed files with 183 additions and 403 deletions.
228 changes: 103 additions & 125 deletions build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -386,123 +386,98 @@ dependencies {
testImplementation "com.google.jimfs:jimfs:1.1"
}

// The --add-open directives required to run GATK. This list needs to be kept in sync with the corresponding
// list in scripts/dockertest.gradle.
//
// These directives need to be:
// - included as properties in the manifest file in the jar(s)
// - passed to java via the gradle "jvmArgs" task property for any task that executes GATK code from a
// classpath that does use a jar (i.e., gradle run, test, javadoc, gatkDoc and jacoco tasks, etc.)
// - passed as java command line args when running from classes directly
// - included in any IntelliJ run/debug/profile configurations
//
final runtimeAddOpens = [
// taken from the union of everything encountered by tests, plus everything defined here:
// https://github.com/apache/spark/blob/v3.3.0/launcher/src/main/java/org/apache/spark/launcher/JavaModuleOptions.java
'java.base/java.lang=ALL-UNNAMED',
'java.base/java.lang.invoke=ALL-UNNAMED',
'java.base/java.lang.reflect=ALL-UNNAMED',
'java.base/java.io=ALL-UNNAMED',
'java.base/java.net=ALL-UNNAMED',
'java.base/java.nio=ALL-UNNAMED',
'java.base/java.util=ALL-UNNAMED',
'java.base/java.util.concurrent=ALL-UNNAMED',
'java.base/java.util.concurrent.atomic=ALL-UNNAMED',
'java.base/sun.nio.ch=ALL-UNNAMED',
'java.base/sun.nio.cs=ALL-UNNAMED',
'java.base/sun.security.action=ALL-UNNAMED',
'java.base/sun.util.calendar=ALL-UNNAMED',
'java.base/sun.nio.fs=ALL-UNNAMED',
'java.base/java.nio.channels.spi=ALL-UNNAMED',
'java.base/jdk.internal.ref=ALL-UNNAMED',
'java.base/java.lang.ref=ALL-UNNAMED',
'java.base/java.util.zip=ALL-UNNAMED',
'java.base/java.util.jar=ALL-UNNAMED',
'java.base/java.nio.file.attribute=ALL-UNNAMED',
'java.base/jdk.internal.loader=ALL-UNNAMED',
'java.base/sun.net.www.protocol.jar=ALL-UNNAMED',
'java.base/sun.invoke.util=ALL-UNNAMED',
'java.base/java.util.concurrent.locks=ALL-UNNAMED',
'java.base/java.security=ALL-UNNAMED',
'java.base/sun.reflect.annotation=ALL-UNNAMED',
'java.base/java.text=ALL-UNNAMED',
'java.base/java.nio.charset=ALL-UNNAMED',
'java.base/sun.reflect.generics.reflectiveObjects=ALL-UNNAMED',
'java.management/com.sun.jmx.mbeanserver=ALL-UNNAMED',
'java.management/javax.management=ALL-UNNAMED',
'java.base/java.util.regex=ALL-UNNAMED',
'java.base/sun.util.locale=ALL-UNNAMED',
'java.base/jdk.internal.math=ALL-UNNAMED',
'java.xml/com.sun.xml.internal.stream.util=ALL-UNNAMED',
'java.base/java.time=ALL-UNNAMED',
'java.base/sun.reflect.generics.factory=ALL-UNNAMED',
'java.base/java.nio.channels=ALL-UNNAMED',
'java.base/sun.security.util=ALL-UNNAMED',
'java.base/java.time.zone=ALL-UNNAMED',
'java.base/sun.reflect.generics.scope=ALL-UNNAMED',
'java.base/sun.reflect.generics.tree=ALL-UNNAMED',
'java.management/com.sun.jmx.interceptor=ALL-UNNAMED',
'java.management/javax.management.openmbean=ALL-UNNAMED',
'java.management/sun.management=ALL-UNNAMED',
'jdk.management/com.sun.management.internal=ALL-UNNAMED',
'jdk.management.jfr/jdk.management.jfr=ALL-UNNAMED',
'jdk.jfr/jdk.jfr.internal.management=ALL-UNNAMED',
'java.base/jdk.internal.module=ALL-UNNAMED',
'java.base/java.lang.module=ALL-UNNAMED',
'java.security.jgss/sun.security.krb5=ALL-UNNAMED'
]

final testAddOpens = [
'java.prefs/java.util.prefs=ALL-UNNAMED' // required for jacoco tasks
]

run {
// taken from the union of everything encountered by tests, plus everything defined here:
// https://github.com/apache/spark/blob/v3.3.0/launcher/src/main/java/org/apache/spark/launcher/JavaModuleOptions.java
jvmArgs = [
'--add-opens', 'java.base/java.lang=ALL-UNNAMED',
'--add-opens', 'java.base/java.lang.invoke=ALL-UNNAMED',
'--add-opens', 'java.base/java.lang.reflect=ALL-UNNAMED',
'--add-opens', 'java.base/java.io=ALL-UNNAMED',
'--add-opens', 'java.base/java.net=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio=ALL-UNNAMED',
'--add-opens', 'java.base/java.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.concurrent=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.concurrent.atomic=ALL-UNNAMED',
'--add-opens', 'java.base/sun.nio.ch=ALL-UNNAMED',
'--add-opens', 'java.base/sun.nio.cs=ALL-UNNAMED',
'--add-opens', 'java.base/sun.security.action=ALL-UNNAMED',
'--add-opens', 'java.base/sun.util.calendar=ALL-UNNAMED',
'--add-opens', 'java.base/sun.nio.fs=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.channels.spi=ALL-UNNAMED',
'--add-opens', 'java.base/jdk.internal.ref=ALL-UNNAMED',
'--add-opens', 'java.base/java.lang.ref=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.zip=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.jar=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.file.attribute=ALL-UNNAMED',
'--add-opens', 'java.base/jdk.internal.loader=ALL-UNNAMED',
'--add-opens', 'java.base/sun.net.www.protocol.jar=ALL-UNNAMED',
'--add-opens', 'java.base/sun.invoke.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.concurrent.locks=ALL-UNNAMED',
'--add-opens', 'java.base/java.security=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.annotation=ALL-UNNAMED',
'--add-opens', 'java.base/java.text=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.charset=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.reflectiveObjects=ALL-UNNAMED',
'--add-opens', 'java.management/com.sun.jmx.mbeanserver=ALL-UNNAMED',
'--add-opens', 'java.management/javax.management=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.regex=ALL-UNNAMED',
'--add-opens', 'java.base/sun.util.locale=ALL-UNNAMED',
'--add-opens', 'java.base/jdk.internal.math=ALL-UNNAMED',
'--add-opens', 'java.xml/com.sun.xml.internal.stream.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.time=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.factory=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.channels=ALL-UNNAMED',
'--add-opens', 'java.base/sun.security.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.time.zone=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.scope=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.tree=ALL-UNNAMED',
'--add-opens', 'java.management/com.sun.jmx.interceptor=ALL-UNNAMED',
'--add-opens', 'java.management/javax.management.openmbean=ALL-UNNAMED',
'--add-opens', 'java.management/sun.management=ALL-UNNAMED',
'--add-opens', 'jdk.management/com.sun.management.internal=ALL-UNNAMED',
'--add-opens', 'jdk.management.jfr/jdk.management.jfr=ALL-UNNAMED',
'--add-opens', 'jdk.jfr/jdk.jfr.internal.management=ALL-UNNAMED',
'--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',
'--add-opens', 'java.prefs/java.util.prefs=ALL-UNNAMED', // jacoco

'-Dio.netty.tryReflectionSetAccessible=true'
]
}
// transform the list of runtime configuration --add-opens args into command line argument format
final runtimeJVMArgs = runtimeAddOpens.stream()
.flatMap(openSpec -> ['--add-opens', openSpec].stream())
.toList()
// add in any other required args
runtimeJVMArgs.add('-Dio.netty.tryReflectionSetAccessible=true')
jvmArgs = runtimeJVMArgs
}

test {
jvmArgs = [
'--add-opens', 'java.base/java.lang=ALL-UNNAMED',
'--add-opens', 'java.base/java.lang.invoke=ALL-UNNAMED',
'--add-opens', 'java.base/java.lang.reflect=ALL-UNNAMED',
'--add-opens', 'java.base/java.io=ALL-UNNAMED',
'--add-opens', 'java.base/java.net=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio=ALL-UNNAMED',
'--add-opens', 'java.base/java.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.concurrent=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.concurrent.atomic=ALL-UNNAMED',
'--add-opens', 'java.base/sun.nio.ch=ALL-UNNAMED',
'--add-opens', 'java.base/sun.nio.cs=ALL-UNNAMED',
'--add-opens', 'java.base/sun.security.action=ALL-UNNAMED',
'--add-opens', 'java.base/sun.util.calendar=ALL-UNNAMED',
'--add-opens', 'java.base/sun.nio.fs=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.channels.spi=ALL-UNNAMED',
'--add-opens', 'java.base/jdk.internal.ref=ALL-UNNAMED',
'--add-opens', 'java.base/java.lang.ref=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.zip=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.jar=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.file.attribute=ALL-UNNAMED',
'--add-opens', 'java.base/jdk.internal.loader=ALL-UNNAMED',
'--add-opens', 'java.base/sun.net.www.protocol.jar=ALL-UNNAMED',
'--add-opens', 'java.base/sun.invoke.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.concurrent.locks=ALL-UNNAMED',
'--add-opens', 'java.base/java.security=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.annotation=ALL-UNNAMED',
'--add-opens', 'java.base/java.text=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.charset=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.reflectiveObjects=ALL-UNNAMED',
'--add-opens', 'java.management/com.sun.jmx.mbeanserver=ALL-UNNAMED',
'--add-opens', 'java.management/javax.management=ALL-UNNAMED',
'--add-opens', 'java.base/java.util.regex=ALL-UNNAMED',
'--add-opens', 'java.base/sun.util.locale=ALL-UNNAMED',
'--add-opens', 'java.base/jdk.internal.math=ALL-UNNAMED',
'--add-opens', 'java.xml/com.sun.xml.internal.stream.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.time=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.factory=ALL-UNNAMED',
'--add-opens', 'java.base/java.nio.channels=ALL-UNNAMED',
'--add-opens', 'java.base/sun.security.util=ALL-UNNAMED',
'--add-opens', 'java.base/java.time.zone=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.scope=ALL-UNNAMED',
'--add-opens', 'java.base/sun.reflect.generics.tree=ALL-UNNAMED',
'--add-opens', 'java.management/com.sun.jmx.interceptor=ALL-UNNAMED',
'--add-opens', 'java.management/javax.management.openmbean=ALL-UNNAMED',
'--add-opens', 'java.management/sun.management=ALL-UNNAMED',
'--add-opens', 'jdk.management/com.sun.management.internal=ALL-UNNAMED',
'--add-opens', 'jdk.management.jfr/jdk.management.jfr=ALL-UNNAMED',
'--add-opens', 'jdk.jfr/jdk.jfr.internal.management=ALL-UNNAMED',
'--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',
'--add-opens', 'java.prefs/java.util.prefs=ALL-UNNAMED', // jacoco

'-Dio.netty.tryReflectionSetAccessible=true'
]
// transform the list test configuration --add-opens (which must include both the runtime and test args) into
// command line argument format
final testJVMAddOpens = new ArrayList<>();
testJVMAddOpens.addAll(runtimeAddOpens);
testJVMAddOpens.addAll(testAddOpens);
final testConfigurationJVMArgs = testJVMAddOpens.stream()
.flatMap(openSpec -> ['--add-opens', openSpec].stream())
.toList()
// add in any other required args
testConfigurationJVMArgs.add('-Dio.netty.tryReflectionSetAccessible=true')
jvmArgs = testConfigurationJVMArgs
}

//add gatk launcher script to the jar as a resource
Expand Down Expand Up @@ -542,6 +517,8 @@ logger.info("build for version:" + version)
group = 'org.broadinstitute'

tasks.withType(Jar) {
// transform the list of --add-opens directives into manifest format
final manifestAddOpens = runtimeAddOpens.stream().collect(java.util.stream.Collectors.joining(" "))
manifest {
attributes 'Implementation-Title': 'The Genome Analysis Toolkit (GATK)',
'Implementation-Version': archiveVersion,
Expand All @@ -550,7 +527,8 @@ tasks.withType(Jar) {
'Picard-Version': picardVersion,
'htsjdk-Version': htsjdkVersion,
'Spark-Version': sparkVersion,
'Multi-Release': 'true'
'Multi-Release': 'true',
'Add-Opens': manifestAddOpens
}
}

Expand Down Expand Up @@ -755,7 +733,7 @@ task testUtilsJar(type: Jar){
//}
//
//javadoc {
// // This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
// // This is a hack to disable the java default javadoc lint until we fix the html formatting
// // We only want to do this for the javadoc task, not gatkDoc
// options.addStringOption('Xdoclint:none', '-quiet')
// source = sourceSets.main.allJava + files(configurations.externalSourceConfiguration.collect { zipTree(it) })
Expand All @@ -764,7 +742,7 @@ task testUtilsJar(type: Jar){
//
//
//task testUtilsJavadoc(type: Javadoc) {
// // This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
// // This is a hack to disable the java default javadoc lint until we fix the html formatting
// // We only want to do this for the javadoc task, not gatkDoc
// options.addStringOption('Xdoclint:none', '-quiet')
// source = sourceSets.testUtils.allJava
Expand Down Expand Up @@ -807,8 +785,8 @@ task testUtilsSourcesJar(type: Jar){
// include '**/*.java'
//
// // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
// // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
// classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
// // runtime classpath.
// classpath = sourceSets.main.runtimeClasspath
// options.docletpath = classpath.asType(List)
// options.doclet = "org.broadinstitute.hellbender.utils.help.GATKHelpDoclet"
//
Expand All @@ -829,7 +807,7 @@ task testUtilsSourcesJar(type: Jar){
// options.addStringOption("build-timestamp", ZonedDateTime.now().format(DateTimeFormatter.RFC_1123_DATE_TIME))
//}
//
//// Generate GATK Bash Tab Completion File
// Generate GATK Bash Tab Completion File
//task gatkTabComplete(type: Javadoc, dependsOn: classes) {
// final File tabCompletionDir = new File("$docBuildDir/tabCompletion")
// doFirst {
Expand All @@ -846,8 +824,8 @@ task testUtilsSourcesJar(type: Jar){
// include '**/*.java'
//
// // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire
// // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives, and Picard.
// classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
// // runtime classpath, includin Picard.
// classpath = sourceSets.main.runtimeClasspath
//
// options.docletpath = classpath.asType(List)
// options.doclet = "org.broadinstitute.barclay.help.BashTabCompletionDoclet"
Expand Down Expand Up @@ -908,8 +886,8 @@ task testUtilsSourcesJar(type: Jar){
// include '**/*.java'
//
// // The gatkWDLGen process instantiates any documented feature classes, so to run it we need the entire
// // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.
// classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles
// // runtime classpath, including picard.
// classpath = sourceSets.main.runtimeClasspath
// options.docletpath = classpath.asType(List)
// options.doclet = "org.broadinstitute.hellbender.utils.help.GATKWDLDoclet"
//
Expand Down

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