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Vertx run results in resource not found error

I am trying to run a vertx server with dynamoDB and lombok annotations, and I am unable to get it to work properly. I have added the .jar files for vertx, dynamoDB, and lombok to my classpath. Everything compiles fine in IntelliJ, but I cannot get it to run properly from my terminal.
I get:
Users-MacBook-Pro:Server User$ vertx run Server.java
java.lang.RuntimeException: Resource not found: Server.java
at io.vertx.core.impl.verticle.CompilingClassLoader.<init>(CompilingClassLoader.java:73)
at io.vertx.core.impl.JavaVerticleFactory.createVerticle(JavaVerticleFactory.java:38)
at io.vertx.core.impl.DeploymentManager.createVerticles(DeploymentManager.java:184)
at io.vertx.core.impl.DeploymentManager.lambda$doDeployVerticle$2(DeploymentManager.java:157)
at io.vertx.core.impl.FutureImpl.checkCallHandler(FutureImpl.java:158)
at io.vertx.core.impl.FutureImpl.setHandler(FutureImpl.java:100)
at io.vertx.core.impl.DeploymentManager.doDeployVerticle(DeploymentManager.java:130)
at io.vertx.core.impl.DeploymentManager.doDeployVerticle(DeploymentManager.java:102)
at io.vertx.core.impl.DeploymentManager.deployVerticle(DeploymentManager.java:90)
at io.vertx.core.impl.VertxImpl.deployVerticle(VertxImpl.java:574)
at io.vertx.core.impl.launcher.commands.VertxIsolatedDeployer.deploy(VertxIsolatedDeployer.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at io.vertx.core.impl.launcher.commands.ClasspathHandler.deploy(ClasspathHandler.java:160)
at io.vertx.core.impl.launcher.commands.RunCommand.deploy(RunCommand.java:389)
at io.vertx.core.impl.launcher.commands.RunCommand.run(RunCommand.java:262)
at io.vertx.core.impl.launcher.VertxCommandLauncher.execute(VertxCommandLauncher.java:230)
at io.vertx.core.impl.launcher.VertxCommandLauncher.dispatch(VertxCommandLauncher.java:365)
at io.vertx.core.impl.launcher.VertxCommandLauncher.dispatch(VertxCommandLauncher.java:328)
at io.vertx.core.Launcher.main(Launcher.java:49)
Failed in deploying verticle
java.lang.RuntimeException: Resource not found: Server.java
at io.vertx.core.impl.verticle.CompilingClassLoader.<init>(CompilingClassLoader.java:73)
at io.vertx.core.impl.JavaVerticleFactory.createVerticle(JavaVerticleFactory.java:38)
at io.vertx.core.impl.DeploymentManager.createVerticles(DeploymentManager.java:184)
at io.vertx.core.impl.DeploymentManager.lambda$doDeployVerticle$2(DeploymentManager.java:157)
at io.vertx.core.impl.FutureImpl.checkCallHandler(FutureImpl.java:158)
at io.vertx.core.impl.FutureImpl.setHandler(FutureImpl.java:100)
at io.vertx.core.impl.DeploymentManager.doDeployVerticle(DeploymentManager.java:130)
at io.vertx.core.impl.DeploymentManager.doDeployVerticle(DeploymentManager.java:102)
at io.vertx.core.impl.DeploymentManager.deployVerticle(DeploymentManager.java:90)
at io.vertx.core.impl.VertxImpl.deployVerticle(VertxImpl.java:574)
at io.vertx.core.impl.launcher.commands.VertxIsolatedDeployer.deploy(VertxIsolatedDeployer.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at io.vertx.core.impl.launcher.commands.ClasspathHandler.deploy(ClasspathHandler.java:160)
at io.vertx.core.impl.launcher.commands.RunCommand.deploy(RunCommand.java:389)
at io.vertx.core.impl.launcher.commands.RunCommand.run(RunCommand.java:262)
at io.vertx.core.impl.launcher.VertxCommandLauncher.execute(VertxCommandLauncher.java:230)
at io.vertx.core.impl.launcher.VertxCommandLauncher.dispatch(VertxCommandLauncher.java:365)
at io.vertx.core.impl.launcher.VertxCommandLauncher.dispatch(VertxCommandLauncher.java:328)
at io.vertx.core.Launcher.main(Launcher.java:49)
java.lang.RuntimeException: Resource not found: Server.java
at io.vertx.core.impl.verticle.CompilingClassLoader.<init>(CompilingClassLoader.java:73)
at io.vertx.core.impl.JavaVerticleFactory.createVerticle(JavaVerticleFactory.java:38)
at io.vertx.core.impl.DeploymentManager.createVerticles(DeploymentManager.java:184)
at io.vertx.core.impl.DeploymentManager.lambda$doDeployVerticle$2(DeploymentManager.java:157)
at io.vertx.core.impl.FutureImpl.checkCallHandler(FutureImpl.java:158)
at io.vertx.core.impl.FutureImpl.setHandler(FutureImpl.java:100)
at io.vertx.core.impl.DeploymentManager.doDeployVerticle(DeploymentManager.java:130)
at io.vertx.core.impl.DeploymentManager.doDeployVerticle(DeploymentManager.java:102)
at io.vertx.core.impl.DeploymentManager.deployVerticle(DeploymentManager.java:90)
at io.vertx.core.impl.VertxImpl.deployVerticle(VertxImpl.java:574)
at io.vertx.core.impl.launcher.commands.VertxIsolatedDeployer.deploy(VertxIsolatedDeployer.java:46)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at io.vertx.core.impl.launcher.commands.ClasspathHandler.deploy(ClasspathHandler.java:160)
at io.vertx.core.impl.launcher.commands.RunCommand.deploy(RunCommand.java:389)
at io.vertx.core.impl.launcher.commands.RunCommand.run(RunCommand.java:262)
at io.vertx.core.impl.launcher.VertxCommandLauncher.execute(VertxCommandLauncher.java:230)
at io.vertx.core.impl.launcher.VertxCommandLauncher.dispatch(VertxCommandLauncher.java:365)
at io.vertx.core.impl.launcher.VertxCommandLauncher.dispatch(VertxCommandLauncher.java:328)
at io.vertx.core.Launcher.main(Launcher.java:49)
Would appreciate some help with this!

This error simply tells you that the Vert.x CLI could not find the Server.java file in the current working directory.
Given that you use Lombok (which modifies code at compile time), I would recommend to run your Verticle after you compiled it with your IDE or build tool.
Here is a list of possibilities to start a Verticle

I was able to fix this issue by creating a fat jar module out of my project. I followed this for help: http://vertx.io/blog/my-first-vert-x-3-application/

JavaFX Graphics Device initialization failed for : es2, sw

So I made small JavaFX project that runs fine in IDE. But when exported in runnable jar in does not run on double click.
In terminal I get following error. I am running Ubuntu 15.04 on 64bit system.
I already did a lot of google search and installed both GTK3 and GTK2 libraries.
I am aware that this is copy of this question but I think it is outdated and non of the methods there have helped me.
I tried adding external jars to my project as gtk.jar, swt.jar, swt-gtk-java3.8.jar and installed every possible library like libswt-gtk-3-java, libgtk2.0, libgtk2.0-dev, libswt-gtk-java-2, libgtk-3-dev, libgtk-3 and libswt-gtk-4-java.
Bellow is detailed error message in terminal using flag -Dprism.verbose=true.
Prism pipeline init order: es2 sw
Using java-based Pisces rasterizer
Using dirty region optimizations
Not using texture mask for primitives
Not forcing power of 2 sizes for textures
Using hardware CLAMP_TO_ZERO mode
Opting in for HiDPI pixel scaling
Prism pipeline name = com.sun.prism.es2.ES2Pipeline
Loading ES2 native library ... prism_es2
GraphicsPipeline.createPipeline failed for com.sun.prism.es2.ES2Pipeline
java.lang.UnsatisfiedLinkError: Can't load library: /home/nemanja/amd64/libprism_es2.so
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1827)
at java.lang.Runtime.load0(Runtime.java:809)
at java.lang.System.load(System.java:1086)
at com.sun.glass.utils.NativeLibLoader.loadLibraryFullPath(NativeLibLoader.java:201)
at com.sun.glass.utils.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:94)
at com.sun.glass.utils.NativeLibLoader.loadLibrary(NativeLibLoader.java:39)
at com.sun.prism.es2.ES2Pipeline.lambda$static$464(ES2Pipeline.java:68)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.prism.es2.ES2Pipeline.<clinit>(ES2Pipeline.java:50)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at com.sun.prism.GraphicsPipeline.createPipeline(GraphicsPipeline.java:187)
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.init(QuantumRenderer.java:91)
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:124)
at java.lang.Thread.run(Thread.java:745)
*** Fallback to Prism SW pipeline
Prism pipeline name = com.sun.prism.sw.SWPipeline
GraphicsPipeline.createPipeline failed for com.sun.prism.sw.SWPipeline
java.lang.UnsatisfiedLinkError: Can't load library: /home/nemanja/amd64/libprism_sw.so
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1827)
at java.lang.Runtime.load0(Runtime.java:809)
at java.lang.System.load(System.java:1086)
at com.sun.glass.utils.NativeLibLoader.loadLibraryFullPath(NativeLibLoader.java:201)
at com.sun.glass.utils.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:94)
at com.sun.glass.utils.NativeLibLoader.loadLibrary(NativeLibLoader.java:39)
at com.sun.prism.sw.SWPipeline.lambda$static$472(SWPipeline.java:42)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.prism.sw.SWPipeline.<clinit>(SWPipeline.java:41)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at com.sun.prism.GraphicsPipeline.createPipeline(GraphicsPipeline.java:187)
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.init(QuantumRenderer.java:91)
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:124)
at java.lang.Thread.run(Thread.java:745)
Graphics Device initialization failed for : es2, sw
Error initializing QuantumRenderer: no suitable pipeline found
java.lang.RuntimeException: java.lang.RuntimeException: Error initializing QuantumRenderer: no suitable pipeline found
at com.sun.javafx.tk.quantum.QuantumRenderer.getInstance(QuantumRenderer.java:280)
at com.sun.javafx.tk.quantum.QuantumToolkit.init(QuantumToolkit.java:221)
at com.sun.javafx.tk.Toolkit.getToolkit(Toolkit.java:205)
at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:209)
at com.sun.javafx.application.LauncherImpl.startToolkit(LauncherImpl.java:675)
at com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:337)
at com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:328)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
Caused by: java.lang.RuntimeException: Error initializing QuantumRenderer: no suitable pipeline found
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.init(QuantumRenderer.java:94)
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:124)
at java.lang.Thread.run(Thread.java:745)
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
Caused by: java.lang.RuntimeException: No toolkit found
at com.sun.javafx.tk.Toolkit.getToolkit(Toolkit.java:217)
at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:209)
at com.sun.javafx.application.LauncherImpl.startToolkit(LauncherImpl.java:675)
at com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:337)
at com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:328)
... 5 more
Short version
Graphics Device initialization failed for : es2, sw
Error initializing QuantumRenderer: no suitable pipeline found
java.lang.RuntimeException: java.lang.RuntimeException: Error initializing QuantumRenderer: no suitable pipeline found
at com.sun.javafx.tk.quantum.QuantumRenderer.getInstance(QuantumRenderer.java:280)
at com.sun.javafx.tk.quantum.QuantumToolkit.init(QuantumToolkit.java:221)
at com.sun.javafx.tk.Toolkit.getToolkit(Toolkit.java:205)
at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:209)
at com.sun.javafx.application.LauncherImpl.startToolkit(LauncherImpl.java:675)
at com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:337)
at com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:328)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
Caused by: java.lang.RuntimeException: Error initializing QuantumRenderer: no suitable pipeline found
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.init(QuantumRenderer.java:94)
at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:124)
at java.lang.Thread.run(Thread.java:745)
Exception in thread "main" java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:767)
Caused by: java.lang.RuntimeException: No toolkit found
at com.sun.javafx.tk.Toolkit.getToolkit(Toolkit.java:217)
at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:209)
at com.sun.javafx.application.LauncherImpl.startToolkit(LauncherImpl.java:675)
at com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:337)
at com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:328)
... 5 more

What's (probably) going wrong
To build executable jar,i use Eclipse export project,runnable jar,package required libraries into jar
Don't use the "package required libraries into jar" to package JavaFX applications. I am not an Eclipse user, but that sounded like a weird option (standard Java packaging does not include library jar files inside your application jar files). So I googled what that option is and came up with this:
Difference between extracting and packaging libraries into a jar file
It seems that the option actually does place libraries inside your application jar and creates some kind of custom class loading system in order to use them.
My guess is that you might have added the jfxrt.jar file as a library file in Eclipse and then it is exported and added to your application jar file by the "package required libraries into jar" option. However jfxrt.jar is not a stand-alone thing, it is not designed to be used outside the directory of the java runtime installation. jfxrt.jar requires binary files (e.g. .so files on unix or .dll files on windows) that interface to the graphics system of the OS in order for JavaFX to function correctly. So you really should not be trying to extract it and use it outside of a JRE installation or a self-contained application.
Solution
What you should do instead is to package your application using any of:
e(fx)clipse packaging.
javafx maven packaging.
javafx ant packaging or the javapackager tool.

Error: Could not find mediaLib accelerator wrapper classes with extension GIS

When I run my NetLogo model with extension GIS in Linux, I obtain this error message:
Error: Could not find mediaLib accelerator wrapper classes. Continuing in pure Java mode.
Occurs in: com.sun.media.jai.mlib.MediaLibAccessor
java.lang.NoClassDefFoundError: com/sun/medialib/mlib/Image
at com.sun.media.jai.mlib.MediaLibAccessor$1.run(MediaLibAccessor.java:248)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.media.jai.mlib.MediaLibAccessor.setUseMlib(MediaLibAccessor.java:245)
at com.sun.media.jai.mlib.MediaLibAccessor.useMlib(MediaLibAccessor.java:177)
at com.sun.media.jai.mlib.MediaLibAccessor.isMediaLibCompatible(MediaLibAccessor.java:357)
at com.sun.media.jai.mlib.MediaLibAccessor.isMediaLibCompatible(MediaLibAccessor.java:315)
at com.sun.media.jai.mlib.MlibScaleRIF.create(MlibScaleRIF.java:67)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at javax.media.jai.FactoryCache.invoke(FactoryCache.java:122)
at javax.media.jai.OperationRegistry.invokeFactory(OperationRegistry.java:1674)
at javax.media.jai.ThreadSafeOperationRegistry.invokeFactory
...
How can I resolve this problem ?

It's a system property, so you'd have to do it at a system level, i.e. by adding -Dcom.sun.media.jai.disableMediaLib=true in your VM Options.

Known issue; see https://github.com/NetLogo/GIS-Extension/issues/4
I don't think this error being printed actually affects anything. Is something not working, or are you just concerned about seeing the error message? If the extension seems to work, I wouldn't worry.

Gradle JRE vs JDK please add lib/tools.jar from your JDK

I'm running java tests with gradle.
here is the exception I have:
java.lang.RuntimeException: java.lang.IllegalStateException: Unable to load Java agent; please add lib/tools.jar from your JDK to the classpath
at org.powermock.modules.agent.PowerMockClassRedefiner.redefine(PowerMockClassRedefiner.java:59)
at org.powermock.modules.agent.support.PowerMockAgentTestInitializer.redefine(PowerMockAgentTestInitializer.java:49)
at org.powermock.modules.agent.support.PowerMockAgentTestInitializer.initialize(PowerMockAgentTestInitializer.java:41)
at com.blablacompany.app.weight.WeightMilestonesViewBeanUnitTest.setUpMock(WeightMilestonesViewBeanUnitTest.java:41)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.runTestClass(JUnitTestClassExecuter.java:80)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassExecuter.execute(JUnitTestClassExecuter.java:47)
at org.gradle.api.internal.tasks.testing.junit.JUnitTestClassProcessor.processTestClass(JUnitTestClassProcessor.java:69)
at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.processTestClass(SuiteTestClassProcessor.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.messaging.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
at org.gradle.messaging.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
at com.sun.proxy.$Proxy2.processTestClass(Unknown Source)
at org.gradle.api.internal.tasks.testing.worker.TestWorker.processTestClass(TestWorker.java:103)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at org.gradle.messaging.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:355)
at org.gradle.internal.concurrent.DefaultExecutorFactory$StoppableExecutorImpl$1.run(DefaultExecutorFactory.java:66)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalStateException: Unable to load Java agent; please add lib/tools.jar from your JDK to the classpath
at org.powermock.modules.agent.JDK6AgentLoader.getVirtualMachineImplementationFromEmbeddedOnes(JDK6AgentLoader.java:97)
at org.powermock.modules.agent.JDK6AgentLoader.loadAgent(JDK6AgentLoader.java:70)
at org.powermock.modules.agent.AgentInitialization.initializeAccordingToJDKVersion(AgentInitialization.java:40)
at org.powermock.modules.agent.PowerMockAgent.verifyInitialization(PowerMockAgent.java:83)
at org.powermock.modules.agent.PowerMockAgent.instrumentation(PowerMockAgent.java:76)
at org.powermock.modules.agent.PowerMockClassRedefiner.redefine(PowerMockClassRedefiner.java:57)
... 37 more
It turns out that for some reason my gradle uses JRE's folder as java.home and this is why it can not find the tools.jar.
I on't think that I want manually add it to my classpath though. I'm wondering if there any way to tell gradle to use JDK's java home instead of JRE's?
I also tried overriding it using org.gradle.java.home in gradle.properties file and it did not work. Any help is greatly appreciated.
WHen I run the same tests from my IDE(Intellij IDEA) all tests are passed successfully. I'm running all it on Mac OS.
println System.getenv("JAVA_HOME")
println System.properties['java.home']
displays:
/Library/Java/JavaVirtualMachines/jdk1.7.0_55.jdk/Contents/Home
/Library/Java/JavaVirtualMachines/jdk1.7.0_55.jdk/Contents/Home/jre

It's not a JDK vs. JRE problem. The values of JAVA_HOME vs. java.home are correct and expected (see other SO question on this topic). tools.jar is necessary to execute tools such as javac and javadoc. However, neither the JDK's javac command line compiler nor Gradle's JavaCompile task will automatically put tools.jar on the compile class path of user code. Instead you'll have to add it explicitly. For example:
def jdkHome = System.getenv("JAVA_HOME")
dependencies {
compile files("$jdkHome/lib/tools.jar")
}

Ok, seems that JRE is actually the right one that I need to use. No reason java.home to be set to JDK.
So the way I solved it was just adding tools library to my classpath:
testCompile ([fileTree(dir: "${System.properties['java.home']}/../lib", include: '*tools.jar'),fileTree(dir: "lib/test", include: '*.jar') ])
Initially the reason why I did not wanted to do this was that once I added it I had a bunch of
java 7 errors: java.lang.VerifyError: Expecting a stackmap frame at branch target 10
I did fix it by adding "-noverify" parameter to my tests closure:
Closure basicTestConfiguration = {
jvmArgs "-Dactivemq.directory=${testActivemqDir}",
"-Duser.timezone=Etc/UTC",
"-javaagent:${configurations.testAgent.singleFile}",
"-XX:MaxPermSize=256m",
"-noverify"
...
}
and applying this closure to my test suite:
postCommitSuite basicTestConfiguration

Edited
Check this out http://www.gradle.org/docs/current/userguide/build_environment.html.
Especially this section
The configuration is applied in following order (in case an option is configured in multiple locations the last one wins):
from gradle.properties located in project build dir.
from gradle.properties located in gradle user home.
from system properties, e.g. when -Dsome.property is used in the command line.

Java EE database Facade Connection Error

I am trying to connect to a database using Facade. I am using Netbeans 7.3.1 JDK 1.7 and JAva EE 7.
There is a Enterprise Application, a client application couple of beans and a class library. I mostly used the insert code method in netbeans to create the connections. I get the following error:
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at org.glassfish.appclient.client.acc.AppClientContainer.launch(AppClientContainer.java:446)
at org.glassfish.appclient.client.AppClientFacade.launch(AppClientFacade.java:183)
atorg.glassfish.appclient.client.AppClientGroupFacade.main(AppClientGroupFacade.java:65)
Caused by: javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:748)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:698)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4475)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2009)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:1979)
at com.sun.ejb.containers.EJBObjectInvocationHandler.invoke(EJBObjectInvocationHandler.java:212)
at com.sun.ejb.containers.EJBObjectInvocationHandlerDelegate.invoke(EJBObjectInvocationHandlerDelegate.java:79)
at com.sun.proxy.$Proxy299.count(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
And
Caused by: java.lang.IllegalArgumentException: No [EntityType] was found for the key class [com.javaee.test.db.Questions] in the Metamodel - please verify that the [Entity] class was referenced in persistence.xml using a specific <class>com.javaee.test.db.Questions</class> property or a global <exclude-unlisted-classes>false</exclude-unlisted-classes> element.
at org.eclipse.persistence.internal.jpa.metamodel.MetamodelImpl.entityEmbeddableManagedTypeNotFound(MetamodelImpl.java:173)
at org.eclipse.persistence.internal.jpa.metamodel.MetamodelImpl.entity(MetamodelImpl.java:193)
at org.eclipse.persistence.internal.jpa.querydef.CommonAbstractCriteriaImpl.internalFrom(CommonAbstractCriteriaImpl.java:114)
at org.eclipse.persistence.internal.jpa.querydef.AbstractQueryImpl.from(AbstractQueryImpl.java:246)
I am not sure where exactly the problem might be so i didn't post any of the code. If you have a hint I can put down the code.

I had the same error last night. I think we are taking the same class! To fix it expand the ejb project -> Configuration Files -> persistence.xml
Under General, there is a checked checkbox "Include All Entity Classes in _ Module". I unchecked the box and then added each class manually. That took care of the exception. Hope this helps.