clover not picking all the java files for instrumentation - using gradle build

[Elizabeth Punnoose]

I have a very big multi project gradle project and I am trying to execute clover on it. I am facing an issue with the instrumentation of the files, the clover is not picking all the files to be instrumented,. The package contains around 10 files and I see only 4 files instrumented at the source-instr folder. 

dependencies {
  testCompile 'junit:junit:4.12'
}
sourceSets {
  clover {
    java {
      srcDir "$buildDir/sources-instr"
    }
  }
}

dependencies {
  cloverCompile 'com.atlassian.clover:clover:4.0.6'
}
configurations { 
  cloverCompile.extendsFrom compile
}
configurations {
  cloverRuntime
  cloverRuntime.extendsFrom cloverCompile
}

task cloverInstr() {
  inputs.files sourceSets.main.allJava 
  outputs.dir "$buildDir/sources-instr"

  doFirst {
    def argsList = ["--initstring", "${rootProject.projectDir}/clover/clover.db",
"-d", "${buildDir}/sources-instr"]
    argsList.addAll(inputs.files.files.collect({ file ->
file.absolutePath
}))
    String[] args = argsList.toArray()
    com.atlassian.clover.CloverInstr.mainImpl(args)
  }
}


cloverInstr.onlyIf { project.hasProperty('clover') }
cloverClasses.dependsOn cloverInstr

test {
  def cloverClasspath = configurations.testRuntime + configurations.cloverRuntime + sourceSets.test.output + sourceSets.clover.output + classpath 
  classpath = cloverClasspath
}

task cloverReport {
  inputs.dir "${buildDir}/clover"
  outputs.dir "${reportsDir}/clover"
  onlyIf {
    file("${buildDir}/clover/clover.db").exists()
  }
  doFirst {
    def argsList = ["--initstring", "${rootProject.projectDir}/clover/clover.db",
"-o", "${reportsDir}/clover/clover.xml","-a"]
    String[] args = argsList.toArray()
    com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
    // com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
  }
}

[Grzegorz Lewandowski]

Are you sure you have all sources in main sources set? As far I can see there's nothing wrong with the setup, but in order to cloverInstr task pick up all source it has to have all sources defined as an input files. Especially, if you generate sources somewhere, then you need to pass them to cloverInstr as-well.