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Gradle Build - Execution failed for task ':sonarqube' can't be indexed twice

I am getting an error "File can't be indexed twice" in gradle build for sonar. Do i have to add any inclusion/exclusion property for sonar? Any help greatly appreciated.
If I take out "src/main/java" in test under sourceSets, I am getting compilation error for junit test cases.
This is how my build.gradle file content look,
group = 'groupid'
apply plugin: 'gradleFortify'
apply plugin: 'org.sonarqube'
apply plugin: 'eclipse'
apply plugin: 'groovy'
apply plugin: 'java'
apply plugin: 'jacoco'
apply plugin: 'groovy'
//apply plugin: "java-library-distribution"
//apply plugin: 'distribution'
version=version
sourceCompatibility = 1.8
repositories {
maven {
url "artifactory"
credentials {
}
}
sonarqube {
properties {
property 'sonar.sourceEncoding', 'UTF-8'
property "sonar.exclusions", ["**/*Test.java"]
}
}
}
buildscript {
repositories {
maven {
url "artifactory"
credentials {
}
}
dependencies {
classpath 'org.jfrog.buildinfo:build-info-extractor-gradle:4.9.7'
classpath 'org.sonarsource.scanner.gradle:sonarqube-gradle-plugin:3.0'
}
}
sourceSets {
main {
java {
srcDirs = ['src/main/java']
}
}
test {
java.srcDirs = ['src/test/java','src/main/java']
}
}
dependencies{
}
task preclean(type: Delete) {
delete 'build'
}
task jcompile(type: JavaCompile) {
dependsOn preclean
source = fileTree(dir: 'src/main/java', include: '**/*.java')
destinationDir = file('build/classes')
sourceCompatibility = '1.8'
targetCompatibility = '1.8'
classpath = configurations.runtime
}
task copyResources( type: Copy ) {
}
task copyClasses( type: Copy ) {
}
jar {
dependsOn jcompile
archiveName = 'prj1.jar'
manifest {
attributes('Implementation-Title': project.name,
'Implementation-Version': project.version)
}
into('lib') {
println "includeInJar: " + configurations.runtime.collect { File file -> file }
from configurations.runtime
}
}
// jar.finalizedBy(jarTask) { }
sonarqube {
properties {
property "sonar.projectName", "prj-${version}"
property "sonar.projectKey", "prj-${version}"
}
}
test {
useJUnitPlatform()
finalizedBy jacocoTestReport
}
jacocoTestReport {
afterEvaluate {
classDirectories = files(classDirectories.files.collect {
fileTree(dir: it, includes: ['com/**'])
})
}
}

The issue described is most likely caused by custom tasks for what Gradle offers out of the box:
Task preclean deletes probably too much. Use clean instead.
Task jcompile compiles the main Java sources which basically duplicates compileJava. The jar task, by default, already depends on compileJava.
I suggest the following:
Remove sourceSets configuration since you're following the convention of using src/main/java and src/test/java.
Remove custom tasks preclean and jcompile.
Cleanup your build script and remove empty tasks copyClasses and copyResources as well as no-op assignment version=version.
From there on, should you have requirements to customize the build, try to resort to what Gradle offers already. You may want to read Building Java & JVM projects first.

Unable to import compiled java avro files into Scala codebase

I am trying to reference the generated Avro files in my scala code basebase. I am using the commercehub avro gradle plugin to generate the avro java compiled files and they get correctly generated in build/generated-main-avro-java/
This is how my gradle file looks. The problem is that the java files get generated correctly but I cannot import them in my scala code. Any idea on what I maybe doing wrong here?
buildscript {
repositories {
gradlePluginPortal()
}
dependencies {
classpath "gradle.plugin.com.lightbend.akka.grpc:akka-grpc-gradle-plugin:0.7.2"
classpath 'com.google.protobuf:protobuf-gradle-plugin:0.8.8'
}
}
plugins {
id 'scala'
id 'application'
id "com.google.protobuf" version "0.8.8"
id 'com.github.johnrengelman.shadow' version '5.2.0'
id "com.commercehub.gradle.plugin.avro" version "0.9.1"
}
apply plugin: 'java'
apply plugin: 'com.lightbend.akka.grpc.gradle'
apply plugin: 'com.google.protobuf'
apply plugin: 'com.github.johnrengelman.shadow'
apply plugin: "com.commercehub.gradle.plugin.avro"
akkaGrpc {
language = "Scala"
generateClient = true
generateServer = true
}
mainClassName = 'com.test.App'
repositories {
mavenLocal()
mavenCentral()
google()
}
tasks.withType(ScalaCompile) {
ScalaCompileOptions.metaClass.daemonServer = true
ScalaCompileOptions.metaClass.fork = true
ScalaCompileOptions.metaClass.useAnt = false
ScalaCompileOptions.metaClass.useCompileDaemon = false
}
def scalaVersion = "2.12"
ext.elasticAPMVersion = "1.14.0"
// Define a separate configuration for managing the dependency on Jetty ALPN agent.
configurations {
alpnagent
}
dependencies {
...
...
...
...
...
implementation "org.apache.avro:avro:1.9.2"
}
test {
jvmArgs "-javaagent:" + configurations.alpnagent.asPath
maxParallelForks = 1
}
run {
mainClassName = mainClassName
standardInput = System.in
}
task runServer(type: JavaExec) {
classpath = sourceSets.main.runtimeClasspath
main = mainClassName
jvmArgs "-javaagent:" + configurations.alpnagent.asPath
}
shadowJar {
classifier = 'shadow'
mainClassName = mainClassName
archiveName = "${title}-${version}.jar"
append 'reference.conf'
destinationDir new File("./docker/bin")
zip64 true
}

I would say, you need to add the generated sources folder to source sets and scala compiler source - something like this:
compileScala {
source = ['src/main/scala', 'src/main/java', 'build/generated-main-avro-java/']
}
sourceSets {
main {
avro {
scala.srcDir file('build/generated-main-avro-java/')
}
}
}

gradle create dependency for maven, build fails

I want to create a sample dependency from project in gradle to project to maven
apply plugin: "maven-publish"
apply plugin: "java"
repositories {
mavenLocal()
}
sourceSets {
main {
java {
srcDirs 'java'
}
resources {
srcDirs 'build'
}
}
}
task sourcesJar(type: Jar) {
from 'build/libs'
classifier = 'sources'
}
publishing {
publications {
maven(MavenPublication) {
groupId = 'or.gradle.sample'
artifactId = 'sort-array'
version = '1.1'
artifact sourcesJar
}
}
repositories {
mavenLocal()
}
}
but when I type:
gradle publishToMavenLocal
I have in log :
... Publishing to repository null ....
and BUILD FAIL

Test package does not read Kotlin classes defined in main package

I cannot seem to access main classes within the test package in my Kotlin module within an Android Studio project. Please note that all code shown below is within a Kotlin JVM module that is imported into the Android app.
Here's my src/main/java code:
import com.google.gson.annotations.SerializedName
data class Customer(val password1: String,
val password2: String,
#SerializedName("last_name") val lastName: String,
#SerializedName("first_name") val firstName: String,
val email: String)
My test code in src/test/java:
class CreateUser {
#Test
fun createRandomUser() {
val random = Random()
val randomNumber = random.nextInt(10000000)
val customer = Customer("password", "password", "lastName", "firstName", "ted$randomNumber#gmail.com")
}
}
My build.gradle code looks like the following:
buildscript {
ext.kotlin_version = '1.1.4-3'
repositories {
mavenCentral()
jcenter()
}
dependencies {
classpath 'me.tatarka:gradle-retrolambda:3.7.0'
classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlin_version"
}
}
apply plugin: 'java'
apply plugin: 'maven'
apply plugin: 'me.tatarka.retrolambda'
apply plugin: 'kotlin'
repositories {
mavenCentral()
jcenter()
}
dependencies {
// some other compile dependencies
compile "org.jetbrains.kotlin:kotlin-stdlib-jre7:$kotlin_version"
testCompile "org.hamcrest:hamcrest-all:1.3"
testCompile 'junit:junit:4.11'
testCompile 'org.mockito:mockito-all:1.9.5'
testCompile "org.jetbrains.kotlin:kotlin-test"
testCompile "org.jetbrains.kotlin:kotlin-test-junit"
}
task javadocJar(type: Jar) {
classifier = 'javadoc'
from javadoc
}
task sourcesJar(type: Jar) {
classifier = 'sources'
from sourceSets.main.allSource
}
artifacts {
archives sourcesJar
archives javadocJar
}
compileKotlin {
kotlinOptions {
jvmTarget = "1.6"
}
}
compileTestKotlin {
kotlinOptions {
jvmTarget = "1.6"
}
}
The root build.gradle file looks as follows:
// Top-level build file where you can add configuration options
common to all sub-projects/modules.
buildscript {
repositories {
jcenter()
}
dependencies {
classpath 'com.android.tools.build:gradle:2.3.3'
// NOTE: Do not place your application dependencies here; they belong
// in the individual module build.gradle files
}
}
allprojects {
repositories {
jcenter()
maven {
url "https://jitpack.io"
credentials { username authToken }
}
}
}
task clean(type: Delete) {
delete rootProject.buildDir
}
ext {
versionName = "0.1.1"
rxJavaVersion = "2.1.3"
okHttpVersion = "3.9.0"
retrofitVersion = "2.3.0"
rxJava2AdapterVersion = "1.0.0"
googleGsonVersion = "2.8.0"
}
The error I get is that gradle cannot resolve Customer (Unresolved reference: Customer) in the Test class. It doesn't seem to include main classes into the test source directory. Yet, it resolves in the IDE.

Ok, I have found the solution. It seems I have to specify the src folders explicitly in my build.gradle and put all Kotlin code in src/main/kotlin and src/test/kotlin respectively.
sourceSets {
main.kotlin.srcDirs = ['src/main/kotlin', 'src/main/java']
main.java.srcDirs = []
test.kotlin.srcDirs = ['src/test/kotlin', 'src/test/java']
test.java.srcDirs = ['src/test/kotlin', 'src/test/java']
}
Once I did that, the tests started to work as expected - reports are even generated on Jenkins which is great.

How to add static files to jar using Gradle build in Spring Boot + Angular 2 project

I have a Spring Boot + Angular 2 project. I want to deploy it to Heroku.
I'm able to run the npm build then copy the generated files over to the public folder (src/resources/public) manually, then run the backend build.
What I want to do is to set up a gradle build that will do all of that at once.
What I have so far is a gradle build that will build the front end, build the backend, however it does not copy the static files before generating the jar. Since the jar does not contain said static files, it won't work on Heroku.
Here's the project folder structure:
root
backend
src/main/java
src/main/resources
frontend
--> angular files go here
build/libs -> where the JAR file goes
The gradle build file:
buildscript {
repositories {
mavenCentral()
}
dependencies {
// spring
classpath('org.springframework.boot:spring-boot-gradle-plugin:1.5.2.RELEASE')
classpath('org.springframework:springloaded:1.2.6.RELEASE')
}
}
plugins {
id "com.moowork.node" version "1.2.0"
}
// gradle wrapper
task wrapper(type: Wrapper) {
gradleVersion = '3.4'
}
// configure gradle-node-plugin
node {
version = '8.1.4'
npmVersion = '5.0.3'
download = true
workDir = file("${project.projectDir}/node")
nodeModulesDir = file("${project.projectDir}/")
}
// clean node/node_modules/dist
task npmClean(type: Delete) {
final def webDir = "${rootDir}/frontend"
delete "${webDir}/node"
delete "${webDir}/node_modules"
delete "${webDir}/dist"
delete "${webDir}/coverage"
delete "${rootDir}/backend/src/main/resources/public"
}
// clean task for npm
task copyFiles {
doLast {
copy {
from "${rootDir}/frontend/dist"
into "${rootDir}/backend/src/main/resources/public"
}
}
}
// build task for npm
task frontendBuild {}
frontendBuild.dependsOn(npm_install)
frontendBuild.dependsOn(npm_run_build)
npm_install {
args = ['--prefix', './frontend']
}
npm_run_build {
args = ['--prefix', './frontend']
}
apply plugin: 'java'
apply plugin: 'eclipse'
apply plugin: 'idea'
apply plugin: 'org.springframework.boot'
sourceSets {
main {
java {
srcDirs = ['backend/src/main/java']
}
resources {
srcDirs = ['backend/src/main/resources']
}
}
}
copyFiles.dependsOn(frontendBuild);
compileJava.dependsOn(frontendBuild);
task backendBuild {}
backendBuild.dependsOn(compileJava)
backendBuild.dependsOn(jar)
jar.dependsOn(copyFiles)
repositories {
mavenCentral()
}
eclipse {
classpath {
containers.remove('org.eclipse.jdt.launching.JRE_CONTAINER')
containers('org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8')
}
}
idea {
module {
inheritOutputDirs = false
outputDir = file("${buildDir}/classes/main/")
}
}
jar {
baseName = 'expense-splitter'
version = '0.0.1'
}
sourceCompatibility = 1.8
targetCompatibility = 1.8
configurations {
dev
}
dependencies {
// spring
compile('org.springframework.boot:spring-boot-starter-web:1.5.2.RELEASE')
compile('org.springframework.boot:spring-boot-starter-data-jpa:1.5.2.RELEASE')
compile('org.springframework.boot:spring-boot-starter-security:1.5.2.RELEASE')
compile('org.apache.commons:commons-lang3:3.3.2')
// to make hibernate handle java 8 date and time types correctly
// it's marked as deprecated but we need to keep it until
// spring boot jpa starts using hibernate 5.2
compile('org.hibernate:hibernate-java8:5.1.0.Final')
// json web tokens
compile ('io.jsonwebtoken:jjwt:0.7.0')
compile 'mysql:mysql-connector-java'
// google gson
compile('com.google.code.gson:gson:2.8.0')
// jackson - parsing of java 8 date and time types
compile('com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.8.7')
// spring dev tools
dev('org.springframework.boot:spring-boot-devtools:1.5.2.RELEASE')
// testing
testCompile('org.springframework.boot:spring-boot-starter-test:1.5.2.RELEASE')
}
// run spring boot app
bootRun {
//addResources = true
classpath = sourceSets.main.runtimeClasspath + configurations.dev
jvmArgs = ["-Xdebug -agentlib:jdwp=transport=dt_socket,address=8080,server=y,suspend=n"]
}
// run all task
task runAll {}
runAll.dependsOn(bootRun)
Thanks in advance,

Try a different approach. Instead of manually copying the resources, tell Gradle that when it processes resources for the JAR, also take into consideration what is in frontend/dist/:
processResources {
from ('frontend/dist/') {
into 'public'
}
}
This should result in a JAR containing a public/ directory, with the contents of frontend/dist/ inside of it.

Gradle configuration for Spring Boot 1.5\2.x + Angular 2-6
Angular in sub-folder frontend
Frontend module
Crate build.gradle:
plugins {
id "com.moowork.node" version "1.2.0"
}
node {
version = '8.11.3'
npmVersion = '5.6.0'
download = true
workDir = file("${project.buildDir}/node")
nodeModulesDir = file("${project.projectDir}")
}
task build(type: NpmTask) {
args = ['run', 'build']
}
build.dependsOn(npm_install)
Note for Angular 6
Update outputPath value in angular.json to 'dist'
Backend module
Edit build.gradle for backend module:
Spring Boot 2.X:
bootJar {
archiveName = "yourapp.jar"
mainClassName = 'com.company.app.Application'
from('frontend/dist') {
into 'static'
}
}
Spring Boot 1.5.X:
jar {
archiveName = "yourapp.jar"
manifest {
attributes 'Main-Class': 'com.company.app.Application'
}
from('frontend/dist') {
into 'static'
}
from {
configurations.compile.collect { it.isDirectory() ? it : zipTree(it) }
}
}
Finally execute bootRepackage or bootJar task and check results in builds/libs

Assume that front end is located at the following folder: src/main/webapp/fe-ui/, the following solution for the Spring Boot version 2.1.1.RELEASE could be considered:
bootJar {
baseName = 'jar-name'
version = '0.1.0'
from('src/main/webapp/fe-ui/build') {
into 'public'
}
}
task installFeDependencies(type: NpmTask) {
args = ['install']
}
task buildFe(type: NpmTask) {
args = ['run', 'build']
dependsOn installFeDependencies
}
compileJava {
dependsOn buildFe
}
Running gradlew build will install, build front end as well as will invoke bootJar. The latter will package built front end bundle.