fix #265: 24.10.x causes stackoverflowerror

.gitignore

@@ -4,7 +4,7 @@
 .gradle
 .idea
 .nextflow*
-gradle.properties
+# gradle.properties
 
 # Ignore Gradle build output directory
 /build/

Makefile

@@ -3,11 +3,13 @@ PROJECT ?= nf-quilt
 WRITE_BUCKET ?= udp-spec
 FRAGMENT ?= &path=.
 NF_DIR ?= ../nextflow
+NF_GIT ?= $(NF_DIR)/nextflow
 NF_BIN ?= ./launch.sh
 PID ?= $$$$
 PIPELINE ?= sarek
 QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
 VERSION ?= $(shell grep 'Plugin-Version' plugins/$(PROJECT)/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
+NXF_VER ?= $(shell cat VERSION)
 TEST_URI ?= quilt+s3://$(WRITE_BUCKET)$(QUERY)\#package=nf-quilt/dest-$(VERSION)$(FRAGMENT)
 PIPE_OUT ?=  quilt+s3://$(WRITE_BUCKET)\#package=$(PROJECT)/$(PIPELINE)
 S3_BASE = s3://$(WRITE_BUCKET)/$(PROJECT)
@@ -30,9 +32,15 @@ check-env:
 clean:
 	./gradlew clean
 	rm -rf null results work
-	rm -rf */*/build plugins/nf-quilt/bin
+	rm -rf build */build */*/build plugins/nf-quilt/bin
 	rm -f .nextflow.log* .launch*classpath
 
+clean-all: clean
+	rm -rf .gradle buildSrc/.gradle
+
+rebuild:
+	./gradlew clean build --refresh-dependencies
+
 compile:
 	./gradlew compileGroovy exportClasspath
 	@echo "DONE `date`"
@@ -107,6 +115,12 @@ $(PIPELINE): $(NF_BIN) install
 	$(NF_BIN) pull nf-core/$(PIPELINE)
 	$(NF_BIN) run nf-core/$(PIPELINE) -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(PIPE_OUT)"
 
+fetchngs: $(NF_GIT)
+	NXF_VER=$(NXF_VER) $(NF_BIN) run quiltdata/fetchngs -r master -profile test,docker --input wf/ids.csv --outdir "s3://$(WRITE_BUCKET)/nf-quilt/fetchngs"
+
+nf-git-ver: $(NF_GIT)
+	NXF_VER=$(NXF_VER) $(NF_GIT) -v
+
 #
 # Show dependencies
 #

VERSION

@@ -1 +1 @@
-23.04.3
+23.10.0

build.gradle

@@ -33,9 +33,14 @@ if (groovyVer) {
             maven { url repo }
         }
 
-        configurations.all {
+        configurations.configureEach {
             resolutionStrategy.eachDependency { DependencyResolveDetails details ->
-                if (details.requested.group == 'org.codehaus.groovy') {
+                force 'cglib:cglib-nodep:3.3.0'
+                force 'org.objenesis:objenesis:3.4'
+
+                // (Optional) If transitive Groovy dependencies cause conflicts
+                force 'org.codehaus.groovy:groovy:3.0.19'
+                if ((details.requested.group == 'org.codehaus.groovy') && details.requested.version != groovyVer) {
                     if (groovyVer.contains(':')) {
                         details.useTarget(groovyVer)
                     }
@@ -49,12 +54,8 @@ if (groovyVer) {
     }
 }
 
-def projects(String...args) {
-    args.collect { project(it) }
-}
 
 group = 'io.nextflow'
-version = rootProject.file('VERSION').text.trim()
 
 allprojects {
     apply plugin: 'java'
@@ -65,17 +66,17 @@ allprojects {
 
     java {
         toolchain {
-            languageVersion = JavaLanguageVersion.of(17)
+            languageVersion = JavaLanguageVersion.of(javaLangVersion)
         }
     }
 
     compileJava {
-        options.release = 11
+        options.release = jdkVersion.toInteger()
     }
 
-    tasks.withType(GroovyCompile) {
-        sourceCompatibility = '1.8'
-        targetCompatibility = '1.8'
+    tasks.withType(GroovyCompile).configureEach {
+        sourceCompatibility = jdkVersion
+        targetCompatibility = jdkVersion
     }
 
     idea {
@@ -98,8 +99,8 @@ allprojects {
 
     dependencies {
         // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
-        implementation 'com.github.groovy-wslite:groovy-wslite:1.1.3'
-        implementation 'org.codehaus.groovy:groovy-all:3.0.23'
+        // implementation 'com.github.groovy-wslite:groovy-wslite:1.1.3'
+        implementation "org.codehaus.groovy:groovy-all:$groovyVersion"
         implementation 'com.fasterxml.jackson.core:jackson-databind:2.18.2'
         implementation 'com.upplication:s3fs:2.2.2'
 
@@ -108,8 +109,8 @@ allprojects {
         }
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.1'
-        groovyDoc 'org.codehaus.groovy:groovy-groovydoc:3.0.23'
-        groovyDoc 'org.codehaus.groovy:groovy-ant:3.0.23'
+        groovyDoc "org.codehaus.groovy:groovy-groovydoc:$groovyVersion"
+        groovyDoc "org.codehaus.groovy:groovy-ant:$groovyVersion"
     }
 
     test {
@@ -127,42 +128,44 @@ allprojects {
     // Disable strict javadoc checks
     // See http://blog.joda.org/2014/02/turning-off-doclint-in-jdk-8-javadoc.html
     if (JavaVersion.current().isJava8Compatible()) {
-        tasks.withType(Javadoc) {
+        tasks.withType(Javadoc).configureEach {
             options.addStringOption('Xdoclint:none', '-quiet')
         }
     }
 
-    tasks.withType(Jar) {
+    tasks.withType(Jar).configureEach {
         duplicatesStrategy = DuplicatesStrategy.INCLUDE
     }
 
     // patched as described here
     // http://forums.gradle.org/gradle/topics/gradle_task_groovydoc_failing_with_noclassdeffounderror
-    tasks.withType(Groovydoc) {
+    tasks.withType(Groovydoc).configureEach {
         groovyClasspath = project.configurations.groovyDoc
         includes = ['nextflow/**']
     }
 
     // Required to run tests on Java 9 and higher in compatibility mode
     if (JavaVersion.current() >= JavaVersion.VERSION_1_9) {
-        tasks.withType(Test) {
-            jvmArgs([
-                    '--add-opens=java.base/java.lang=ALL-UNNAMED',
-                    '--add-opens=java.base/java.io=ALL-UNNAMED',
-                    '--add-opens=java.base/java.nio=ALL-UNNAMED',
-                    '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
-                    '--add-opens=java.base/java.net=ALL-UNNAMED',
-                    '--add-opens=java.base/java.util=ALL-UNNAMED',
-                    '--add-opens=java.base/java.util.concurrent.locks=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.fs=ALL-UNNAMED',
-                    '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
-                    '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
-                    '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
-                    '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
-                    '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
-            ])
+        tasks.withType(Test).tap {
+            configureEach {
+                jvmArgs([
+                        '--add-opens=java.base/java.lang=ALL-UNNAMED',
+                        '--add-opens=java.base/java.io=ALL-UNNAMED',
+                        '--add-opens=java.base/java.nio=ALL-UNNAMED',
+                        '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
+                        '--add-opens=java.base/java.net=ALL-UNNAMED',
+                        '--add-opens=java.base/java.util=ALL-UNNAMED',
+                        '--add-opens=java.base/java.util.concurrent.locks=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.fs=ALL-UNNAMED',
+                        '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
+                        '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
+                        '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
+                        '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
+                        '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
+                ])
+            }
         }
     }
 }
@@ -195,8 +198,8 @@ task exportClasspath {
     dependsOn allprojects.jar
     doLast {
         def all = getRuntimeConfigs()
-        def libs = all.collect { File file -> file.canonicalPath;  }
-        ['nextflow', 'nf-commons', 'nf-httfs'].each { libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath }
+        def libs = all.collect { File file -> file.canonicalPath  }
+        ['nextflow', 'nf-commons', 'nf-httfs'].each { libs << file("modules/$it/build/libs/${it}-${nextflowVersion}.jar").canonicalPath }
         file('.launch.classpath').text = libs.unique().join(':')
     }
 }

buildSrc/build.gradle

@@ -0,0 +1,14 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Support convention plugins written in Groovy. Convention plugins are build scripts in 'src/main' that automatically become available as plugins in the main build.
+    id 'groovy-gradle-plugin'
+}
+
+repositories {
+    // Use the plugin portal to apply community plugins in convention plugins.
+    gradlePluginPortal()
+}
+

buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle

@@ -0,0 +1,11 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.nextflow.groovy-common-conventions'
+
+    // Apply the application plugin to add support for building a CLI application in Java.
+    id 'application'
+}

buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle

@@ -0,0 +1,53 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the groovy Plugin to add support for Groovy.
+    id 'groovy'
+}
+
+repositories {
+    // Use Maven Central for resolving dependencies.
+    mavenCentral()
+}
+
+ext {
+    jdkVersion = '11'
+    javaLangVersion = 19
+}
+
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(javaLangVersion) // from nf-schema
+    }
+}
+
+compileJava {
+    options.release.set(jdkVersion.toInteger())
+}
+
+tasks.withType(GroovyCompile) {
+    sourceCompatibility = jdkVersion
+    targetCompatibility = jdkVersion
+}
+
+tasks.withType(Test) {
+    jvmArgs ([
+            '--add-opens=java.base/java.lang=ALL-UNNAMED',
+            '--add-opens=java.base/java.io=ALL-UNNAMED',
+            '--add-opens=java.base/java.nio=ALL-UNNAMED',
+            '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
+            '--add-opens=java.base/java.net=ALL-UNNAMED',
+            '--add-opens=java.base/java.util=ALL-UNNAMED',
+            '--add-opens=java.base/java.util.concurrent.locks=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.fs=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
+            '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
+            '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
+    ])
+}

buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle

@@ -0,0 +1,11 @@
+/*
+ * This file was generated by the Gradle 'init' task.
+ */
+
+plugins {
+    // Apply the common convention plugin for shared build configuration between library and application projects.
+    id 'io.nextflow.groovy-common-conventions'
+    // Apply the java-library plugin for API and implementation separation.
+    id 'java-library'
+}
+

gradle.properties

@@ -0,0 +1,4 @@
+nextflowVersion = 23.10.0
+groovyVersion = 3.0.19
+jdkVersion = 11
+javaLangVersion = 19

groovysh-task.gradle

@@ -3,10 +3,10 @@ gradle.projectsLoaded {
         afterEvaluate { project ->
             if (!project.repositories.any { it.name == 'MavenRepo' }) {
                 project.repositories {
-                    // To be able to load org.apache.groovy:groovy-groovysh and dependencies
+                    // To be able to load org.codehaus.groovy:groovy-groovysh and dependencies
                     mavenCentral {
                         content {
-                            includeGroup 'org.apache.groovy'
+                            includeGroup 'org.codehaus.groovy'
                             includeGroup 'jline'
                             includeGroup 'com.github.javaparser'
                             includeGroup 'org.ow2.asm'
@@ -21,7 +21,7 @@ gradle.projectsLoaded {
             }
 
             project.dependencies {
-                groovyshdependencies 'org.apache.groovy:groovy-groovysh:4.0.24'
+                groovyshdependencies 'org.codehaus.groovy:groovy-groovysh:4.0.24'
             }
 
             project.tasks.register('groovysh') {
@@ -35,7 +35,7 @@ gradle.projectsLoaded {
 
                     def groovyshClass
                     def groovyShell
-                    groovyshClass = Class.forName('org.apache.groovy.groovysh.Groovysh', true, groovyshClassLoader)
+                    groovyshClass = Class.forName('org.codehaus.groovy.groovysh.Groovysh', true, groovyshClassLoader)
                     if (groovyshClass) {
                         groovyShell = groovyshClass.newInstance()
                         if (groovyShell) {