Code works in JavaSE, but crashes in Wildfly with NullPointerException

Question

I'm generating graphs with gephi-toolkit (0.9.1), wrote a javaSE application fine, tested it and so on.

While copy-pasting this code to my EJB (tried all three types) the code starts producing:

java.lang.RuntimeException: java.lang.NullPointerException

on exporting graph to SVG (and PNG also).

I explicitly check my objects - they are not null. So, something deep inside of gephi-toolkit is compatible with JavaSE and not with JavaEE.

Any hints or recommendations how to find and fix problem?

I tried to export to File (File.createTempFile()) then to stream - StringWriter and OutputStream. All three failed.

ExportController ec = Lookup.getDefault().lookup(ExportController.class);
SVGExporter exp = (SVGExporter) ec.getExporter("svg");
StringWriter sw = new StringWriter();
exp.setWriter(sw);
exp.setWorkspace(workspace);
System.out.println(" exec: " + exp.execute());

ec, exp and sw are not null, but I get NPE on exp.execute()

Update:

java.lang.RuntimeException: java.lang.NullPointerException at org.gephi.io.exporter.preview.SVGExporter.execute(SVGExporter.java:113) at model.GraphBuilder.generateGraph(GraphBuilder.java:155) 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 org.jboss.as.ee.component.ManagedReferenceMethodInterceptor.processInvocation(ManagedReferenceMethodInterceptor.java:52) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.InterceptorContext$Invocation.proceed(InterceptorContext.java:437) at org.jboss.as.weld.ejb.Jsr299BindingsInterceptor.doMethodInterception(Jsr299BindingsInterceptor.java:82) at org.jboss.as.weld.ejb.Jsr299BindingsInterceptor.processInvocation(Jsr299BindingsInterceptor.java:93) at org.jboss.as.ee.component.interceptors.UserInterceptorFactory$1.processInvocation(UserInterceptorFactory.java:63) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.invocationmetrics.ExecutionTimeInterceptor.processInvocation(ExecutionTimeInterceptor.java:43) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.jpa.interceptor.SBInvocationInterceptor.processInvocation(SBInvocationInterceptor.java:47) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.InterceptorContext$Invocation.proceed(InterceptorContext.java:437) at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:64) at org.jboss.as.weld.ejb.EjbRequestScopeActivationInterceptor.processInvocation(EjbRequestScopeActivationInterceptor.java:83) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ee.concurrent.ConcurrentContextInterceptor.processInvocation(ConcurrentContextInterceptor.java:45) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.InitialInterceptor.processInvocation(InitialInterceptor.java:21) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.ChainedInterceptor.processInvocation(ChainedInterceptor.java:61) at org.jboss.as.ee.component.interceptors.ComponentDispatcherInterceptor.processInvocation(ComponentDispatcherInterceptor.java:52) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.pool.PooledInstanceInterceptor.processInvocation(PooledInstanceInterceptor.java:51) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.tx.CMTTxInterceptor.invokeInOurTx(CMTTxInterceptor.java:275) at org.jboss.as.ejb3.tx.CMTTxInterceptor.required(CMTTxInterceptor.java:327) at org.jboss.as.ejb3.tx.CMTTxInterceptor.processInvocation(CMTTxInterceptor.java:239) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.interceptors.CurrentInvocationContextInterceptor.processInvocation(CurrentInvocationContextInterceptor.java:41) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.invocationmetrics.WaitTimeInterceptor.processInvocation(WaitTimeInterceptor.java:47) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.security.SecurityContextInterceptor.processInvocation(SecurityContextInterceptor.java:100) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.deployment.processors.StartupAwaitInterceptor.processInvocation(StartupAwaitInterceptor.java:22) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.interceptors.ShutDownInterceptorFactory$1.processInvocation(ShutDownInterceptorFactory.java:64) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.interceptors.LoggingInterceptor.processInvocation(LoggingInterceptor.java:67) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ee.component.NamespaceContextInterceptor.processInvocation(NamespaceContextInterceptor.java:50) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.as.ejb3.component.interceptors.AdditionalSetupInterceptor.processInvocation(AdditionalSetupInterceptor.java:54) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.ContextClassLoaderInterceptor.processInvocation(ContextClassLoaderInterceptor.java:64) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.InterceptorContext.run(InterceptorContext.java:356) at org.wildfly.security.manager.WildFlySecurityManager.doChecked(WildFlySecurityManager.java:636) at org.jboss.invocation.AccessCheckingInterceptor.processInvocation(AccessCheckingInterceptor.java:61) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.InterceptorContext.run(InterceptorContext.java:356) at org.jboss.invocation.PrivilegedWithCombinerInterceptor.processInvocation(PrivilegedWithCombinerInterceptor.java:80) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.ChainedInterceptor.processInvocation(ChainedInterceptor.java:61) at org.jboss.as.ee.component.ViewService$View.invoke(ViewService.java:198) at org.jboss.as.ee.component.ViewDescription$1.processInvocation(ViewDescription.java:185) at org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:340) at org.jboss.invocation.ChainedInterceptor.processInvocation(ChainedInterceptor.java:61) at org.jboss.as.ee.component.ProxyInvocationHandler.invoke(ProxyInvocationHandler.java:73) at model.GraphBuilder$$$view20.generateGraph(Unknown Source) at beans.Controller.submit3(Controller.java:193) 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 com.sun.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:181) at com.sun.el.parser.AstValue.invoke(AstValue.java:289) at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:304) at org.jboss.weld.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40) at org.jboss.weld.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50) at org.jboss.weld.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40) at org.jboss.weld.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50) at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:105) at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:87) at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102) at javax.faces.component.UICommand.broadcast(UICommand.java:315) at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:790) at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1282) at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:81) at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101) at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:198) at javax.faces.webapp.FacesServlet.service(FacesServlet.java:658) at io.undertow.servlet.handlers.ServletHandler.handleRequest(ServletHandler.java:85) at io.undertow.servlet.handlers.security.ServletSecurityRoleHandler.handleRequest(ServletSecurityRoleHandler.java:62) at io.undertow.servlet.handlers.ServletDispatchingHandler.handleRequest(ServletDispatchingHandler.java:36) at org.wildfly.extension.undertow.security.SecurityContextAssociationHandler.handleRequest(SecurityContextAssociationHandler.java:78) at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) at io.undertow.servlet.handlers.security.SSLInformationAssociationHandler.handleRequest(SSLInformationAssociationHandler.java:131) at io.undertow.servlet.handlers.security.ServletAuthenticationCallHandler.handleRequest(ServletAuthenticationCallHandler.java:57) at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) at io.undertow.security.handlers.AbstractConfidentialityHandler.handleRequest(AbstractConfidentialityHandler.java:46) at io.undertow.servlet.handlers.security.ServletConfidentialityConstraintHandler.handleRequest(ServletConfidentialityConstraintHandler.java:64) at io.undertow.security.handlers.AuthenticationMechanismsHandler.handleRequest(AuthenticationMechanismsHandler.java:60) at io.undertow.servlet.handlers.security.CachedAuthenticatedSessionHandler.handleRequest(CachedAuthenticatedSessionHandler.java:77) at io.undertow.security.handlers.NotificationReceiverHandler.handleRequest(NotificationReceiverHandler.java:50) at io.undertow.security.handlers.AbstractSecurityContextAssociationHandler.handleRequest(AbstractSecurityContextAssociationHandler.java:43) at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) at org.wildfly.extension.undertow.security.jacc.JACCContextIdHandler.handleRequest(JACCContextIdHandler.java:61) at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) at io.undertow.server.handlers.PredicateHandler.handleRequest(PredicateHandler.java:43) at io.undertow.servlet.handlers.ServletInitialHandler.handleFirstRequest(ServletInitialHandler.java:292) at io.undertow.servlet.handlers.ServletInitialHandler.access$100(ServletInitialHandler.java:81) at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:138) at io.undertow.servlet.handlers.ServletInitialHandler$2.call(ServletInitialHandler.java:135) at io.undertow.servlet.core.ServletRequestContextThreadSetupAction$1.call(ServletRequestContextThreadSetupAction.java:48) at io.undertow.servlet.core.ContextClassLoaderSetupAction$1.call(ContextClassLoaderSetupAction.java:43) at io.undertow.servlet.api.LegacyThreadSetupActionWrapper$1.call(LegacyThreadSetupActionWrapper.java:44) at io.undertow.servlet.api.LegacyThreadSetupActionWrapper$1.call(LegacyThreadSetupActionWrapper.java:44) at io.undertow.servlet.api.LegacyThreadSetupActionWrapper$1.call(LegacyThreadSetupActionWrapper.java:44) at io.undertow.servlet.api.LegacyThreadSetupActionWrapper$1.call(LegacyThreadSetupActionWrapper.java:44) at io.undertow.servlet.api.LegacyThreadSetupActionWrapper$1.call(LegacyThreadSetupActionWrapper.java:44) at io.undertow.servlet.handlers.ServletInitialHandler.dispatchRequest(ServletInitialHandler.java:272) at io.undertow.servlet.handlers.ServletInitialHandler.access$000(ServletInitialHandler.java:81) at io.undertow.servlet.handlers.ServletInitialHandler$1.handleRequest(ServletInitialHandler.java:104) at io.undertow.server.Connectors.executeRootHandler(Connectors.java:202) at io.undertow.server.HttpServerExchange$1.run(HttpServerExchange.java:805) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:748) ERROR [stderr] (default task-11) Caused by: java.lang.NullPointerException at org.gephi.preview.plugin.renderers.NodeLabelRenderer.renderSVG(NodeLabelRenderer.java:277) at org.gephi.preview.plugin.renderers.NodeLabelRenderer.render(NodeLabelRenderer.java:198) at org.gephi.preview.PreviewControllerImpl.render(PreviewControllerImpl.java:251) at org.gephi.preview.PreviewControllerImpl.render(PreviewControllerImpl.java:208) at org.gephi.io.exporter.preview.SVGExporter.execute(SVGExporter.java:95)

workspace is not null also. :( I thought that 2KB of code of creating graph is not relevant. — Oleg Gritsak
The stacktrace says the NPE occurs in NodeLabelRenderer.java:277, so the logical thing to do is to make sure you have the source code for gephi (not just the toolkit), and then start your application from your IDE in debug mode (or attach a remote debugger). Without your code and a debugger, I can only speculate, but looking at the source code, the issue could be related to XML parsers - perhaps the Xalan or Stax dependency conflicts with something on the Application server. — Klaus Groenbaek

Hugues M. Hugues M. · Accepted Answer · 2017-06-04T22:48:39

Executive summary: code works on desktop but fails on server because server is in headless mode, and code uses some functionality (here getBBox()) within Batik that requires a GUI.

A major difference between your code running in a simple Java SE program, and the same code running in a server environment, is that the latter is most likely headless.

Gephi delegates to Batik for SVG generation, and in turn Batik uses java.awt for some rendering details, and rendering is (likely) necessary for bounding box computation (getBBox()), which unfortunately gephi relies on.

Old versions of Batik used to crash on headless environments. Now it mostly works. See this example in Batik source code:

/**
 * Returns the active screen resolution. If Batik is run in a headless environment, this
 * method will return the default "96" unlike {@link Toolkit#getScreenResolution()} which
 * will throw a {@link HeadlessException}.
 * @return the screen resolution in dpi
 */
public static int getScreenResolution() {
    if (GraphicsEnvironment.isHeadless()) {
        return 96;
    } else {
        return Toolkit.getDefaultToolkit().getScreenResolution();
    }
}

But it seems still limited when trying to compute a bounding box.

So, one suggestion worth trying, if possible (depending in your situation, it might be very easy, or very complicated): start your server in a non-headless environment.

Wildfly (and most servers) by default runs with -Djava.awt.headless=true in the command line. It should be possible to change that by editing standalone.conf.

For this to work you'll need a display. For example on Linux, give it a valid $DISPLAY to use, that would point to a virtual display, like a VNC server, or better with Virtual Framebuffer, which is a 'fake' X server (avoids X-windows on server, CentOS package is xorg-x11-server-xvfb, Debian's is xvfb).

Maybe that is not a satisfactory solution for production, but if it works, it will at least be a good clue to help determine where to look next: how to get getBBox() work in headless environment, or have gephi work without needing getBBox().

Code works in JavaSE, but crashes in Wildfly with NullPointerException

1 Answers