Develop Reference

JAXBContextFactory hell - java.lang.ClassNotFoundException: com.ibm.xml.xlxp2.jaxb.JAXBContextFactory

I keep getting the following error in my dev environment. I use
Eclipse Mars 4.5.1
Oracle JDK 1.7 (build 1.7.0_79-b15) or 1.8 (build 1.8.0_65-b17)
Apache Ant to run the code as well as Eclipse to run the code
Ivy for dependency management where I include the following
<!-- 3rd party dependencies -->
<dependency org="log4j" name="log4j" rev="1.2.16" conf="test->default"/>
<dependency org="commons-httpclient" name="commons-httpclient" rev="3.1" conf="compile->default"/>
<dependency org="org.jvnet.jaxb2_commons" name="jaxb2-basics-runtime" rev="0.6.4" conf="default->runtime"/>
<dependency org="org.jvnet.jaxb2_commons" name="jaxb2-basics-tools" rev="0.6.4" conf="default->runtime"/>
<dependency org="org.jvnet.jaxb2_commons" name="jaxb2-basics" rev="0.6.4" conf="default->runtime"/>
I've seen the other posts on this topic but their answers don't help much. I tried using a jaxb.properties but that did not change the behavior.
javax.xml.bind.context.factory=com.sun.tools.xjc.runtime.JAXBContextFactory
Exception in thread "main" javax.xml.bind.JAXBException
- with linked exception:
[java.lang.ClassNotFoundException: com.ibm.xml.xlxp2.jaxb.JAXBContextFactory]
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:227)
at javax.xml.bind.ContextFinder.find(ContextFinder.java:432)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:637)
at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:584)
at com.acme.merge.util.ProjectsInformation.unMarshal(ProjectsInformation.java:24)
at com.acme.merge.controller.MergeController.main(MergeController.java:44)
Caused by: java.lang.ClassNotFoundException: com.ibm.xml.xlxp2.jaxb.JAXBContextFactory
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at javax.xml.bind.ContextFinder.safeLoadClass(ContextFinder.java:563)
at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:225)
... 5 more
What am I overlooking?

I found the root cause. Some of my dependencies in ivy have transitive dependencies that bring in some IBM WS libraries. These libraries override my settings and force the use of com.ibm.xml.xlxp2.jaxb.JAXBContextFactory. Excluding these resolved my issue.
The conflicting jar is from package com.ibm.ws and is called runtime.jar.

The solution that seem to work for me :
https://java.wekeepcoding.com/article/19606872/Issue+in+creating+an+instance+of+JAX-WS+client+to+access+the+service
The Missing class "com.ibm.xml.xlxp2.jaxb.JAXBContextFactory" is available in the jar "com.ibm.jaxws.thinclient_8.5.0.jar" which will be available in the server runtime directory for Websphere App server : C:\Program Files\IBM\WebSphere\AppServer\runtimes.
Please include this jar for compile purpose only and donot include this in your WAR or EAR as it will conflict with your server runtime library jar.
For server WAS 8.0 the path jar would be "com.ibm.jaxws.thinclient_8.0.0.jar".

Nutch: NoClassDefFoundError: org/springframework/retry/RetryCallback

I am running the normal Nutch indexing, it used to work 2 days ago perfectly but today out of nowhere it just stopped working with the previous error. Following the stack error:
Exception in thread "main" java.lang.NoClassDefFoundError: org/springframework/retry/RetryCallback
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
at java.lang.Class.getConstructor0(Class.java:3075)
at java.lang.Class.newInstance(Class.java:412)
at org.apache.nutch.plugin.Extension.getExtensionInstance(Extension.java:161)
at org.apache.nutch.indexer.IndexWriters.<init>(IndexWriters.java:55)
at org.apache.nutch.indexer.IndexingJob.index(IndexingJob.java:121)
at org.apache.nutch.indexer.IndexingJob.run(IndexingJob.java:228)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:70)
at org.apache.nutch.indexer.IndexingJob.main(IndexingJob.java:238)
Caused by: java.lang.ClassNotFoundException: org.springframework.retry.RetryCallback
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 10 more
I ended up seeing that the error occurred at this exact piece of code :
Object object = extensionClazz.newInstance();
Another question on SO but with different project was able to fix the issue by adding the spring-framework-messaging dependency
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-messaging</artifactId>
<version>4.2.4.RELEASE</version>
</dependency>
well i am using nutch version 1.12 with ivy for dependency management so in my config is the following:
<dependency org="org.springframework.retry" name="spring-retry" rev="1.2.0.RELEASE">
<exclude module="spring-beans"/>
<exclude module="spring-context"/>
<exclude module="spring-core"/>
<exclude module="spring-aop"/>
</dependency>
and even with adding the spring-messaging dependency it's still not working.
Any ideas?

These kind of errors might come when you have more than one version of same jar (same class) in your classpath, You can see the dependency tree by executing
<report conf="compile" /> for ivy projects
And
mvn dependency:tree for maven projects
Narrow down to the version that you want and you can exclude the other jar by explicitly excluding that jar from the module which is importing it .

No idea what went wrong but this was able to fix the problem
ant clean
ant runtime

Ivy CleanCache Task throwing NullPointException

I have the following project directory structure:
MyProject/
src/main/java/
All of my Java sources
build/
build.xml
build.properties
ivy.xml
ivy-settings.xml
ivy-settings.properties
The build.xml looks like this:
<project name="MyProject" default="audit" basedir=".." xmlns:ivy="antlib:org.apache.ivy.ant">
<property file="build/build.properties"/>
<property environment="env"/>
<path id="ant.lib.path">
<fileset dir="${env.ANT_HOME}/lib" includes="*.jar"/>
</path>
<taskdef resource="org/apache/ivy/ant/antlib.xml" uri="antlib:org.apache.ivy.ant" classpathref="ant.lib.path"/>
<target name="configIvy">
<echo message="Configuring Ivy."/>
<echo message="URL is: ${ivy.settings.home}"/>
<ivy:settings url="${ivy.settings.home}"/>
<!-- Clear/flush the Ivy cache. -->
<echo message="Cleaning the local Ivy cache for the current build."/>
<ivy:cleancache/>
</target>
</project>
When I run ant -buildfile /<path-to-my-project>/MyProject/build/build.xml configIvy, I get the following console output:
Buildfile: /<path-to-my-project>/MyProject/build/build.xml
configIvy:
[echo] Configuring Ivy.
[echo] URL is: file:////<path-to-my-project>/MyProject/build/ivy-settings.xml
[ivy:cleancache] :: Apache Ivy 2.3.0-rc1 - 20120416000235 :: http://ant.apache.org/ivy/ ::
BUILD FAILED
/<path-to-my-project>/MyProject/build/build.xml:85: java.lang.ExceptionInInitializerError
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:169)
at org.apache.ivy.util.url.URLHandlerRegistry.getHttp(URLHandlerRegistry.java:47)
at org.apache.ivy.ant.IvyAntSettings.configureURLHandler(IvyAntSettings.java:367)
at org.apache.ivy.ant.IvyAntSettings.createIvyEngine(IvyAntSettings.java:267)
at org.apache.ivy.ant.IvyAntSettings.getConfiguredIvyInstance(IvyAntSettings.java:237)
at org.apache.ivy.ant.IvyTask.getIvyInstance(IvyTask.java:92)
at org.apache.ivy.ant.IvyTask.prepareTask(IvyTask.java:256)
at org.apache.ivy.ant.IvyTask.execute(IvyTask.java:276)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:392)
at org.apache.tools.ant.Target.performTasks(Target.java:413)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
at org.apache.tools.ant.Project.executeTarget(Project.java:1368)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1251)
at org.apache.tools.ant.Main.runBuild(Main.java:811)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.NullPointerException
at org.apache.log4j.Category.isDebugEnabled(Category.java:129)
at org.apache.commons.logging.impl.Log4JLogger.isDebugEnabled(Log4JLogger.java:239)
at org.apache.commons.httpclient.HttpClient.<clinit>(HttpClient.java:69)
... 25 more
My ivy-settings.xml file specifies a URL resolver of an Artifactory repo that is hosted on my local machine (http://localhost:8080/artifactory/myrepo). I'm wondering if Ivy uses HttpClient under the hood (as the stacktrace suggests), and for some reason, is choking because its an HTTP URL on the same machine? Maybe?!? And yes, I'm sure that the URL is correct and that Artifactory is running while I run the Ant build!
Can anyone spot what is going on here? Why would <ivy-cleancache> throw a NPE? I'm looking at its source code and can't seem to find where the NPE is coming from, or why. I can supply more details if needed. Thanks in advance!

I thought I gave a response to this, but I don't see it here...
Don't put extra jars for your projects into $ANT_HOME/lib. There are several reasons for this:
As you've found out, there can be jar clash as each set of optional tasks tries to setup the classpath they need. Yes, it's nice not having to set a classpath when you do a <taskdef>, but it's not that bad.
If you give your project to someone else, they'll have to install all of the optional jars too before they can do a build.
The better way is to create a ${basedir}/ant.lib directory, and then put each set of ant task jars in their own sub-directory. For example, you'd put Ivy jars in ${basedir}/ant.lib/ivy and you put Checkstyle jars in ${basedir}/ant.lib/checkstyle. Then, you define your taskdef with a classpath pointing to the directory like this:
<taskdef resource="org/apache/ivy/ant/antlib.xml"
uri="antlib:org.apache.ivy.ant">
<classpath>
<fileset dir="${basedir}/lib/ivy"/>
</classpath>
</taskdef>
This way, Ivy doesn't pick up the wrong jars. As a bonus, you can also give someone your project, and Ivy is already installed and running for them. No need for them to download Ivy and setup the jar in the right classpath.
By the way, $ANT_HOME/lib is already in the Ant classpath, so if you didn't specify a classpath, all the jars in $ANT_HOME/lib will be picked up automatically. You could have simply done this:
<taskdef resource="org/apache/ivy/ant/antlib.xml"
uri="antlib:org.apache.ivy.ant"/>
with no classpath required.

Java NoClassDefFoundError despite set classpath

I have some trouble with getting a Java application to run in the console and/or with Ant.
I know that a lot of starting issues are related to the classpath being not set or incorrectly set, though I'm fairly sure I set it correctly, so my search only yielded results on that.
Here is the general setup of my application:
classes are in packages model, view and controller. controller.Controller is the class with the main method. I am using objectdb as my JPA provider.
I am using Ant to compile my application.
After compiling, I can run my application from ant with the following script:
<target name="run" description="default build process">
<java fork="true" classname="${main-class}">
<classpath>
<path refid="classpath" />
</classpath>
</java>
</target>
where ${main-class} is controller.Controller and classpath consists of /lib and /dist folders (the application's jar file is compiled to /dist)
Now I tried copying all .jar files from /lib and /dist to one separate folder and run them withjava -jar cooking.jar -cp . which results in
Exception in thread "main" java.lang.NoClassDefFoundError: javax/persistence/Persistence
at model.jpa.JPAModelFactory.<init>(JPAModelFactory.java:28)
at model.jpa.JPAModelFactory.<init>(JPAModelFactory.java:24)
at controller.Controller.<init>(Controller.java:59)
at controller.Controller.main(Controller.java:116)
Caused by: java.lang.ClassNotFoundException: javax.persistence.Persistence
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 4 more
So I tried ant and slightly modified above build target to:
<target name="run2" description="default build process">
<java fork="true" jar="${dist.dir}/${ant.project.name}.jar">
<classpath>
<path refid="classpath" />
</classpath>
</java>
</target>
which results in the same error. I don't understand why.
Just to test it, I tried running from the command line by specifying the main class directly: java -cp . controller.Controller which for some reason cannot even locate the class (it's there, I confirmed it):
Exception in thread "main" java.lang.NoClassDefFoundError: controller/Controller
Caused by: java.lang.ClassNotFoundException: controller.Controller
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Could not find the main class: controller.Controller. Program will exit.
I have set JAVA_HOME to my JDK's path, and CLASSPATH to my JRE's/lib path.
OS is Windows 7 64 bit, Java version is 1.6.0_25-b06
I am puzzled by two things:
a) Why is Java unable to locate controller.Controller, even though it is present in the .jar file and the .jar file is in the current directory?
b) What am I doing wrong that calling Java with -jar seems to mess up the lookup mechanisms.
Any help is highly appreciated.

The class path should consist of
directories with class files (in their proper package directory)
jar files.
You cannot point the class path to a directory of jars. Things are different when running a application server (eg Tomcat), which will load jars from a directory for you.

though I'm fairly sure I set it correctly
The evidence is against you. The JVM is telling you that you have not set it correctly.
What do you think that ref 'classpath' pointing to? Where do you assume its values are coming from? They should be defined inside the Ant build.xml, right? Like this:
<path id="production.class.path">
<pathelement location="${production.classes}"/>
<pathelement location="${production.resources}"/>
<fileset dir="${production.lib}">
<include name="**/*.jar"/>
<exclude name="**/junit*.jar"/>
<exclude name="**/*test*.jar"/>
</fileset>
</path>
<path id="test.class.path">
<path refid="production.class.path"/>
<pathelement location="${test.classes}"/>
<pathelement location="${test.resources}"/>
<fileset dir="${test.lib}">
<include name="**/junit*.jar"/>
<include name="**/*test*.jar"/>
</fileset>
</path>
If you're creating an executable JAR, you need to specify the main class and classpath in the manifest, as CoolBeans correctly pointed out in the comment. The 3rd party JAR locations have to be relative to the executable JAR. You should package them with your executable JAR in such a way that the relative path is easy to sort out and understand.

I've found this happens when I specify both the <classpath> and the jar="..." in the target. I removed the jar="...", placed that .jar into the <classpath> list and it ran after that.

is it possible to load jars-in-jars in JWS?

I have found MANY threads on packing all dependencies along with the project into one jar package, and it seems like there are many different ways to achieve this (oneJar, FatJar, Ant-build...)
So cooking up my own recipe, I have (after quite some effort) managed to package the project I am working on. In this one jar file, there is the code for the project plus all the jars that the project depends on which are loaded with jar-in-jar-loader that comes with eclipse. The resultant works fine on a number of different platforms, when it's ran through the terminal invoked via java -jar myjarfile.
Peachy, you might say, here's the problem though; when I sign my jar and try to run it via javaws (which is the ultimate goal here) I get an exception which I have decrypted to mean that libraries (in the case below org.apache.commons.lang.SystemUtils) are unaccessible.
So here's my question; is it not possible to load jars in jars when the applications is deployed for Java Web Start? If it is possible, what am I doing wrong? If not, what's the best alternative?
Thanks!
Below is the JNLP file along with the stackTrace I get when I run javaws myJNLPfile
<?xml version="1.0" encoding="utf-8"?>
<jnlp spec="1.0+"
codebase="file:///home/ukirik/workspace/myproject/dist"
href="project.jnlp">
<information>
<!-- Project info -->
</information>
<security>
<all-permissions />
</security>
<resources os="Mac\ OS\ X">
<j2se version="1.6+" java-vm-args="-XstartOnFirstThread"/>
</resources>
<resources>
<jar href="myjar-jws.jar" />
</resources>
<application-desc main-class="org.gvt.RuntimeMain"/>
</jnlp>
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.sun.javaws.Launcher.executeApplication(Launcher.java:1799)
at com.sun.javaws.Launcher.executeMainClass(Launcher.java:1745)
at com.sun.javaws.Launcher.doLaunchApp(Launcher.java:1507)
at com.sun.javaws.Launcher.run(Launcher.java:129)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.NoClassDefFoundError: org/apache/commons/lang/SystemUtils
at org.gvt.RuntimeMain.loadSwtJar(RuntimeMain.java:27)
at org.gvt.RuntimeMain.main(RuntimeMain.java:13)
... 9 more
Caused by: java.lang.ClassNotFoundException: org.apache.commons.lang.SystemUtils
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at com.sun.jnlp.JNLPClassLoader.findClass(JNLPClassLoader.java:332)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
... 11 more

If you are using the Eclipse jar-in-jar loader I think that you may need this in the jnlp file
<application-desc main-class="org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader"/>
That's assuming that your manifest is looking like this...
Manifest-Version: 1.0
Ant-Version: Apache Ant 1.7.1
Created-By: 20.1-b02 (Sun Microsystems Inc.)
Main-Class: org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader
Rsrc-Main-Class: yourapp.mainclass
Rsrc-Class-Path: ./ swt.jar velocity-1.7-dep.jar
Class-Path: .

It seems like the problem is with the classloader.
You may want to use a custom classloader in JWS, as described here:
http://lopica.sourceforge.net/faq.html#customcl
Depending on exactly what you need to do, in terms of packaging, there are a couple of options.

The problem you're running into is that you're passing org.gvt.RuntimeMain as your main class for your jar in your JNPL file, but that's a one-jar jar. Because it's a one-jar jar, you need to provide class com.simontuffs.onejar.Boot instead, as
<application-desc main-class="com.simontuffs.onejar.Boot"/>
The reason for it, is that the one-jar plugin will generate that class, which will make use of a classloader that understands jars within jars, and then invoke your org.gvt.RuntimeMain class (it figures it out through looking at the manifests's One-Jar-Main-Class: header).