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Recreation of jpa metamodels

I want to use JPA meta-models in my project. I added required dependency to my project, added generation to JavaCompile task and meta-models are successfully generated. If I want to run the code again, It doesn't compile. It fails with:
Error:java: Problem with Filer: Attempt to recreate a file for type project.models.AdministrationUser_
for every single meta-model. I am running it in Idea as spring boot run. If I use gradle task boot run than it will run just fine, no problem, but I need Idea run, because I need to set active profiles. It also shows, that problem is probably not in code but somewhere in run task configuration but I have no idea what to change and I tried to change several things but I'm just firing blanks.
I'm using Gradle 5.4.1., Idea 2019.2 and Java 11.
Here are important parts of my build.gradle file:
dependencies {
annotationProcessor("javax.xml.bind:jaxb-api")
annotationProcessor("org.hibernate:hibernate-jpamodelgen")
}
tasks.withType(JavaCompile) {
options.annotationProcessorGeneratedSourcesDirectory =
file("src/generated/java")
}
sourceSets {
generated {
java {
srcDirs = ['src/generated/java']
}
}
}
Something similar was already asked here but one answer suggest to delete hibernate-jpamodelgen what (if I understand it correctly) seems like absurd solution - because it wont work if you delete it. Other answer suggest using some maven plugin, so not an option for me either.
I'm stuck on this problem for a longer time, have no one to talk to about it and I'm completely out of ideas so I'm pretty desperate and any help will be much appreciated.

First, make modifications to your build.gradle.
You point to the wrong directory in the sourceSets section. Fix it:
sourceSets {
generated {
java {
srcDirs = ['src/generated']
}
}
}
Then make further improvements:
With Gradle 5.2 and Intellij 2019.1 annotationProcessors is the only piece of configuration you need. See https://github.com/tbroyer/gradle-apt-plugin/blob/v0.21/README.md
Get rid of
tasks.withType(JavaCompile) {
options.annotationProcessorGeneratedSourcesDirectory =
file("src/generated/java")
}
sourceSets {
generated {
java {
srcDirs = ['src/generated/java']
}
}
}
Lastly, consider delegating your build and test tasks to Gradle (this is now the default). Go to File -> Settings -> Build, Execution, Deployment -> Build Tools -> Gradle -> Build and run using Gradle

Gradle task not running as demanded (before compiling)

INTRODUCTION
The project is in Kotlin and builds using Gradle. I'm trying to generate a basic data class with some build info, let's say for now that I need it [re]generated every time before running.
Here's the Gradle task I have now:
def generatedDir = "$buildDir/generated"
// noinspection GroovyAssignabilityCheck
task generateBuildInfo {
inputs.property "version", rootProject.version.toString()
inputs.property "name", rootProject.name.toString()
outputs.dir generatedDir
outputs.upToDateWhen { false }
doFirst {
def buildInfoFile = file("$generatedDir/BuildInfo.kt")
buildInfoFile.parentFile.mkdirs()
buildInfoFile.text = """
internal data class BuildInfo(
val version: String = "${project.version.toString() ?: "unspecified"}",
val name: String = "${project.name.toString() ?: "unspecified"}"
)
""".replace(" ", "").trim()
}
}
To be able to resolve this from IntelliJ IDEA, I added my new folder to project sources, and obviously wired up the dependencies, like so:
sourceSets.main.kotlin.srcDirs += generatedDir
project.afterEvaluate {
compileJava.dependsOn generateBuildInfo
compileKotlin.dependsOn generateBuildInfo
}
This is all done in a separate file (to avoid polluting my main scripts). Due to this organization, after applying plugins, I just include the generator in my main script, like this:
apply from: "gradle/scripts/build-info-generator.gradle"
THE PROBLEM
It looks like the generator code is executed only once, after running assemble when I first ran clean on this module. This is not what I want, because when I change some of the project properties (like version), the source does not get updated... as if compileJava/compileKotlin and my custom task are not executed.
They do not appear in build logs as executed.
Is there any way I can run this task every time I want to run my module's launcher? Sure, I can do some smart file comparison to see if generation is needed, but for now I just want it done each time. Am I missing something?

IDEA has its own build system, indepenant from Gradle.
You can configure it to run a Gradle task before its own build task.
You can also configure it to delegate all the build/run tasks to Gradle. But that's not the default.

Gradle: Add dependency from Java to Native compilation

I try to setup gradle for a proper JNI compilation, so I need to build first a shared library (with the c plugin), and then compile and test the java code (which consumes the library).
Here a sample of the build.gradle, related to the native compilation:
model {
components {
yli(NativeLibrarySpec) {
sources {
c {
source {
srcDir 'src/main/c'
include "Yli.c"
commonFolders.each {
include "$it/**/*.c"
}
}
}
}
buildTypes {
release
}
}
}
}
What is the best way to tell gradle that the compileJava should wait for the build of the NativeLibrarySpec?
Edit: When I try to add
compileJava.dependsOn(yliSharedLibrary)
I have the following error during gradle build:
* What went wrong:
A problem occurred evaluating root project 'yli'.
> Could not get unknown property 'sharedLibrary' for root project 'yli' of type org.gradle.api.Project.
Note: I used the command 'gradle tasks' in order to found the name of the task: 'yliSharedLibrary'.

I played around with this and discovered that you can access the tasks created by the software model within closures. For example, if you want to depend on one of the native tasks, you can do so with:
compileJava.dependsOn { yliNativeCompileTask }
Of course, if you want the Java task to come after the native one, but not force an actual dependency between them, you can use mustRunAfter():
compileJava.mustRunAfter { yliNativeCompileTask }
This syntax also works for declared inputs and outputs:
compileJava.inputs.files { yliNativeCompileTask }
Note that if you tie the inputs of a task to the outputs of another task, you don't have to explicitly declare a dependsOn. Gradle infers the task dependency.
Disclaimer I don't know if this is the correct way to do this, or how far you can take this approach.
One final thing: the old native software model is being replaced by a new set of native plugins based on Gradle's original model. It should be much easier to integrate Java projects with these new plugins, but you may want to wait until the plugins have been fully fleshed out before attempting a migration.

Annotation processor in Gradle outputs source files to build/classes making javadoc fail. How to fix it?

I have an annotation processor that is automatically picked up by the Java compiler at build time (using SPI). During a gradle build, the generated java sources of this annotation processor are put in build/classes as Gradle tells the annotation processor that this is the place to output generated source files.
When the standard javadoc task is run, it tries to create javadoc for all files in build/classes, including *.java. This failes because javadoc only expects *.class files, making the whole build fail.
So my question is:
Is this a Gradle bug/feature?
How do I fix it/make it work?

It seems the problem is that the generated source files are not picked up, making the javadoc fail because it had nothing to process.
I'm posting the solution here in case somebody is experiencing the same problem:
The problem with compile time source generation in gradle is that the outputted sources are not automatically picked up by the javadoc. This is a problem if all your sources are auto generated. The build will fail with an error saying that no sources could be processed. In the other case your build will succeed but you will have no javadoc of your generated java sources.
The root problem here is gradle's poor integration with generating sources that are both generated and compiled during the same compile step. To remedy this I changed my build files to this.
project layout:
rootproject
rootproject/annotationProcessor
rootproect/userOfAnnotationProcessor
build file of userOfAnnotationProcessor
def generatedSources = "$buildDir/generated-src"
def generatedOutputDir = file("$generatedSources")
compileJava {
doFirst {
generatedOutputDir.exists() || generatedOutputDir.mkdirs()
options.compilerArgs = [
'-s', "${generatedSources}"
]
}
}
sourceSets {
main {
java {
srcDirs += generatedOutputDir
}
}
}
javadoc {
source = sourceSets.main.resources
}
compileJava.dependsOn clean
The trick here is to not add your generated sources to a custom sources set, else we'll run into troubles when trying to build aggregated javadoc in our root project. However this solution has the nasty side effect that our generated sources or added twice for some reason when trying to build after a first clean+build. The solution here is to always do a clean+build.
Now when doing an aggregate javadoc build, we'd like our generated source javadoc to be part of it as well.
This is how our rootproject build file looks like:
def exportedProjects = [
":annotationProcessor",
":userOfAnnotationProcessor",
]
task alljavadoc(type: Javadoc) {
source exportedProjects.collect { project(it).sourceSets.main.allJava }
classpath = files(exportedProjects.collect { project(it).sourceSets.main.compileClasspath })
destinationDir = file("${buildDir}/docs/javadoc")
}
alljavadoc.dependsOn(":userOfAnnotationProcessor:compileJava")
If we had used a custom source set previously, gradle would now start complaining about source set properties not being found. Why? I don't know... A last important thing to notice is that our alljavadoc depeonds on the compilation step of userOfAnnotationProcessor, this is needed to make sure our generated source files are there when the aggregated javadoc is build.
I hope I've helped sombody with this explanation!

I am not quite sure weather it is a bug or not. But as a workaround just filter the sources of javadoc.
Depending on how your build script looks like, it should look something like thistask
myJavadocs(type: Javadoc) {
classpath = sourceSets.main.output.filter { it -> !it.name.endsWith('.java') }
}

Dynamically add JAR to Gradle dependencies

Currently, my build.gradle has a dependency on an external library built with Ant. To accomplish building the library, I followed the advice here and created a task which builds the external library, and copies it to the libs/ folder.
The task is called as part of a dependency:
build.gradle
dependencies {
compile fileTree('libs') {
include '*.jar'
builtBy 'myTask'
}
}
task myTask (type: GradleBuild) { GradleBuild antBuild ->
antBuild.buildFile('external-stub.gradle')
antBuild.tasks = ['clean', 'ivy.check', 'ivy.download', 'ivy.task', 'ivy',
'init', 'mergeCode', 'compile', 'jar', 'copyJarsToProject']
}
However, when the compile actually runs, the library I just built and copied in is not included in the dependencies, as evidenced by a whole lot of compilation errors.
Am I including the library the wrong way?
The full build.gradle and associated files are over at Github, and I've linked to the specific commit I'm having issues with: Source Repository

Alright, took me a while to get a build I was happy with. But, here's what was changed.
The actual build of the JAR was built using the same style, but moved to the external project (so that the main build project wasn't reaching across to it). I'll give an in-depth explanation below, but the commits are here and here. These are in order.
Basically, we export the jar as an artifact that other projects can depend on, rather than copying over the Jar ourselves. This way, the Ant build runs and other projects can see the Jar we just created. This is the end of the first commit. In the second commit, the task outputs are marked as needing to be regenerated only if the Jar does not exist. This was due to the fact that whenever I tried to build the app, it would take minutes to regen the Jar, and then have to repackage everything else as well. The code is below:
build.gradle External Project
configurations {
buildJSword
}
task doBuildJSword (type: GradleBuild) {
buildFile = 'jsword-stub.gradle'
tasks = ['clean', 'ivy.check', 'ivy.download', 'ivy.task', 'ivy',
'init', 'mergeCode', 'compile', 'jar'] //, 'copyJarsToMinimalBible']
ext.outputJar = file('distribution/jsword.jar')
outputs.upToDateWhen {
ext.outputJar.exists()
}
}
artifacts {
buildJSword(doBuildJSword.ext.outputJar) {
builtBy doBuildJSword
}
}
Then, the main project just has to add this project as a compile-time dependency:
build.gradle Main Project
compile project(path: ':jsword-minimalbible', configuration: 'buildJSword')
Hope this is helpful for anyone with a similar issue, let me know if you have questions!
Note: The build currently does not clean itself properly, so if you change any code in the external project, you need to delete the external Jar for everything to regenerate itself correctly.