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how to resolve "java.util.zip.ZipException:duplicate entry: org/apache/xmlbeans/xml/stream/Location.class" issue while hosting springboot in tomcat 10

I am trying to host spring boot rest api in Apache Tomcat 10, but it is not getting hosted, I had placed my spring boot application in webapps-javaee folder, as tomcat 10 default support jakartaee
When I checked logs I am getting this err
23-Mar-2022 19:48:49.103 SEVERE [Catalina-utility-2] org.apache.tomcat.jakartaee.Migration.migrateArchiveStreaming Failed to migrate archive [webService-0.0.1-SNAPSHOT-exec.war]. Using the "-zipInMemory" option may help.
java.util.zip.ZipException: duplicate entry: org/apache/xmlbeans/xml/stream/Location.class
at java.util.zip.ZipOutputStream.putNextEntry(Unknown Source)
at org.apache.tomcat.jakartaee.Migration.migrateArchiveStreaming(Migration.java:228)
at org.apache.tomcat.jakartaee.Migration.migrateStream(Migration.java:289)
at org.apache.tomcat.jakartaee.Migration.migrateArchiveStreaming(Migration.java:229)
at org.apache.tomcat.jakartaee.Migration.migrateStream(Migration.java:289)
at org.apache.tomcat.jakartaee.Migration.migrateFile(Migration.java:200)
at org.apache.tomcat.jakartaee.Migration.execute(Migration.java:166)
at org.apache.catalina.startup.HostConfig.migrateLegacyApp(HostConfig.java:1298)
at org.apache.catalina.startup.HostConfig$MigrateApp.run(HostConfig.java:2048)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(Unknown Source)
at org.apache.catalina.startup.HostConfig.migrateLegacyApps(HostConfig.java:1260)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:471)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1757)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:316)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1162)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1365)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1369)
at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1347)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.runAndReset(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(Unknown Source)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
my Spring boot application is working fine in tomcat 9, but for tomcat 10 it is giving this error

You have to convert the war file manually, go to https://tomcat.apache.org/download-migration.cgi and download the migration tool, then run the command java -jar jakartaee-migration-1.0.0-shaded.jar -zipInMemory oldFile.war newFile.war, the -zipInMemory option will take care of duplicated files in your war file, then you can put the new war file directly in the webapps folder.

Problem with dependencies in ResourceConfig on Jersey

I have a Jersey / Spring project (Project A : com.project.a) on Eclipse that depends on another (Project B : com.project.b).
Eclipse does not show any error on the projects until building and running the application on a local Tomcat server.
It throws this error:
SEVERE: StandardWrapper.Throwable
MultiException stack 1 of 1
java.lang.NoClassDefFoundError: com/project/b/SomeClassToRegister
at com.project.a.CustomApplication.<init>(CustomApplication.java:31)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at org.glassfish.hk2.utilities.reflection.ReflectionHelper.makeMe(ReflectionHelper.java:1129)
at org.jvnet.hk2.internal.Utilities.justCreate(Utilities.java:1009)
at org.jvnet.hk2.internal.ServiceLocatorImpl.create(ServiceLocatorImpl.java:905)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:997)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:989)
at org.glassfish.jersey.server.ApplicationHandler.createApplication(ApplicationHandler.java:340)
at org.glassfish.jersey.server.ApplicationHandler.<init>(ApplicationHandler.java:319)
at org.glassfish.jersey.servlet.WebComponent.<init>(WebComponent.java:336)
at org.glassfish.jersey.servlet.ServletContainer.init(ServletContainer.java:170)
at org.glassfish.jersey.servlet.ServletContainer.init(ServletContainer.java:358)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1228)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1172)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1066)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5449)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5747)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1707)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1697)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: com.project.b.SomeClassToRegister
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1955)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1798)
... 28 more
Jul 09, 2019 5:52:13 PM org.apache.catalina.core.StandardContext loadOnStartup
SEVERE: Servlet [com.project.a.CustomApplication] in web application [/someApplication] threw load() exception
java.lang.ClassNotFoundException: com.project.b.SomeClassToRegister
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1955)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1798)
at com.project.a.CustomApplication.<init>(CustomApplication.java:31)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at org.glassfish.hk2.utilities.reflection.ReflectionHelper.makeMe(ReflectionHelper.java:1129)
at org.jvnet.hk2.internal.Utilities.justCreate(Utilities.java:1009)
at org.jvnet.hk2.internal.ServiceLocatorImpl.create(ServiceLocatorImpl.java:905)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:997)
at org.jvnet.hk2.internal.ServiceLocatorImpl.createAndInitialize(ServiceLocatorImpl.java:989)
at org.glassfish.jersey.server.ApplicationHandler.createApplication(ApplicationHandler.java:340)
at org.glassfish.jersey.server.ApplicationHandler.<init>(ApplicationHandler.java:319)
at org.glassfish.jersey.servlet.WebComponent.<init>(WebComponent.java:336)
at org.glassfish.jersey.servlet.ServletContainer.init(ServletContainer.java:170)
at org.glassfish.jersey.servlet.ServletContainer.init(ServletContainer.java:358)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1228)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1172)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1066)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5449)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5747)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1707)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1697)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
CustomApplication extends org.glassfish.jersey.server.ResourceConfig and is trying to register that class as follows:
public class CustomApplication extends ResourceConfig {
public CustomApplication() {
// Specify packages of java code.
packages("com.project.a");
packages("com.project.b"); //>>> Line 30
register(com.project.b.SomeClassToRegister.class); //>>> Line 31
}
}
Interestingly, Line 30 calls the main package of com.project.b with no problem, but the code crashes on line 31. com.project.b.SomeClassToRegister exists on the dependency com.project.b .
After the error is shown, the welcome-file jsp page for the server is shown normally, but every endpoint throws the same NoClassDefFoundError error when accessed.
The build path of Project A has Project B as a listed dependency and Project B is also listed as part of the Web Deployment Assembly packaging of Project A.
I am currently running it on a local Tomcat server with the following resource configuration. I have tried to remove the duplicate appearance of Project B with the same result.
Am I missing anything about linking the two projects together that might be the cause of the error?

After fiddling a lot with the configurations of both projects, what worked for me was :
Go to Properties of Project A
Java Build Path
Source
Add folder src/main/java of Project B
Apply and close
Clean projects and run

Embedded Tomcat failed to scan

I work on Eclipse with an embedded Tomcat (8.0.24). I ran mvn clean package install and got a build success.
However, when I start tomcat by running a main method in Eclipse (as it's an embedded Tomcat), I got lots of error like :
mai 11, 2018 3:26:20 PM org.apache.tomcat.util.scan.StandardJarScanner processURLs
WARNING: Failed to scan [file:/C:/Users/username/.m2/repository/com/sun/xml/ws/jaxws-rt/2.1.7/saaj-impl.jar] from classloader hierarchy
java.io.FileNotFoundException: C:\Users\username\.m2\repository\com\sun\xml\ws\jaxws-rt\2.1.7\saaj-impl.jar (The system cannot find the file specified)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.<init>(Unknown Source)
at java.util.zip.ZipFile.<init>(Unknown Source)
at java.util.jar.JarFile.<init>(Unknown Source)
at java.util.jar.JarFile.<init>(Unknown Source)
at org.apache.tomcat.util.compat.JreCompat.jarFileNewInstance(JreCompat.java:188)
at org.apache.tomcat.util.scan.JarFileUrlJar.<init>(JarFileUrlJar.java:65)
at org.apache.tomcat.util.scan.JarFactory.newInstance(JarFactory.java:49)
at org.apache.tomcat.util.scan.StandardJarScanner.process(StandardJarScanner.java:374)
at org.apache.tomcat.util.scan.StandardJarScanner.processURLs(StandardJarScanner.java:309)
at org.apache.tomcat.util.scan.StandardJarScanner.doScanClassPath(StandardJarScanner.java:266)
at org.apache.tomcat.util.scan.StandardJarScanner.scan(StandardJarScanner.java:229)
at org.apache.catalina.startup.ContextConfig.processJarsForWebFragments(ContextConfig.java:1888)
at org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1116)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:765)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:299)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:94)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5138)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1421)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1411)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
I listed some of the concerned .jar :
com\sun\xml\bind\jaxb-xjc\2.1.7\jsr173_1.0_api.jar
com\sun\xml\bind\jaxb-xjc\2.1.7\activation.jar
com\sun\xml\bind\jaxb-xjc\2.1.7\jaxb-impl.jar
com\sun\xml\bind\jaxb-xjc\2.1.7\jaxb-api.jar
com\sun\xml\bind\jaxb-xjc\2.1.7\activation.jar
com\sun\xml\bind\jaxb-impl\2.1.7\jaxb1-impl.jar
com\sun\xml\bind\jaxb-impl\2.1.7\jsr173_1.0_api.jar
com\sun\xml\bind\jaxb-impl\2.1.7\activation.jar
com\sun\xml\bind\jaxb-impl\2.1.7\jaxb-api.jar
com\sun\xml\messaging\saaj\saaj-impl\1.3.3\activation.jar
com\sun\xml\messaging\saaj\saaj-impl\1.3.3\saaj-api.jar
com\sun\xml\ws\jaxws-rt\2.1.7\stax-utils.jar
com\sun\xml\ws\jaxws-rt\2.1.7\streambuffer.jar
com\sun\xml\ws\jaxws-rt\2.1.7\stax-ex.jar
com\sun\xml\ws\jaxws-rt\2.1.7\activation.jar
com\sun\xml\ws\jaxws-rt\2.1.7\jaxb-impl.jar
com\sun\xml\ws\jaxws-rt\2.1.7\jaxb-api.jar
com\sun\xml\ws\jaxws-rt\2.1.7\resolver.jar
com\sun\xml\ws\jaxws-rt\2.1.7\woodstox.jar
com\sun\xml\ws\jaxws-rt\2.1.7\sjsxp.jar
com\sun\xml\ws\jaxws-rt\2.1.7\jsr173_api.jar
com\sun\xml\ws\jaxws-rt\2.1.7\saaj-impl.jar
com\sun\xml\ws\jaxws-rt\2.1.7\saaj-api.jar
com\sun\xml\ws\jaxws-rt\2.1.7\jsr250-api.jar
com\sun\xml\ws\jaxws-rt\2.1.7\jsr181-api.jar
com\sun\xml\ws\jaxws-rt\2.1.7\jaxws-api.jar
javax\xml\soap\saaj-api\1.3\servlet.jar
javax\xml\soap\saaj-api\1.3\jax-qname.jar
javax\xml\soap\saaj-api\1.3\activation.jar
javax\xml\soap\saaj-api\1.3\jaxp-api.jar
I already deleted the content of repository in .m2 and eclipse->project->maven->update project->update project (and force update of snapshot/release).
I checked in the indicated locations and indeed those .jar don't exist. I am a maven's beginner so maybe my error is stupid...

java web start application unable to launch on java7u45

After the upgrade to java7u45 from java7u21 , there have been a lot of security related changes done.
So first there were warnings related to missing attributes in manifest files. Fixed it by following previously provided solution .
Permissions: all-permissions
Codebase: *
Application-Name: My Name
Added the attributes to the MANIFEST file and re-signed them all.
Now when I launch the application using my jnlp file, it gives following error on this particular jar
Error: Unable to load resource
http://<path>/org.eclipse.core.filesystem.win32.x86_<version>.jar
java.io.IOException: Invalid signature file digest for Manifest main attributes
at com.sun.deploy.cache.CacheEntry$10.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.deploy.cache.CacheEntry.writeFileToDisk(Unknown Source)
at com.sun.deploy.cache.CacheEntry.writeFileToDisk(Unknown Source)
at com.sun.deploy.cache.Cache.downloadResourceToTempFile(Unknown Source)
at com.sun.deploy.cache.Cache.downloadResourceToCache(Unknown Source)
at com.sun.deploy.net.DownloadEngine.actionDownload(Unknown Source)
at com.sun.deploy.net.DownloadEngine.downloadResource(Unknown Source)
at com.sun.deploy.cache.ResourceProviderImpl.getResource(Unknown Source)
at com.sun.deploy.cache.ResourceProviderImpl.getResource(Unknown Source)
at com.sun.javaws.LaunchDownload$DownloadTask.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Verified the manifest file for this jar for missing attributes and signed it again. But same error .
Any pointers ?

This org.eclipse*.jar and some other eclipse jar files have their own Signature Files (ECLIPSEF.SF) in the META-INF/ directory.
Since this extra SF file still has the SHA-DIGEST of the previous MANIFEST main attributes(which were now changed) , the plugin is failing to load.
Remove these and other signature files from all the plugins and re-sign them. :-)

error while deploy app with tomcat

I have developed an app and now am trying to deployed it on Tomcat. when I start start.bat file in Tomcat directory. My console doesn't display any errors and when I open log files, I see this error:
java.lang.ClassNotFoundException: com.sun.xmk.ws.transport.http.servlet.WSServletContextListener
On many forums people say that I didn't add jaxws-rt.jar lib. But I have added it. First I added it as a dependency in maven. After that I deleted the dependency and downloaded the library from official site and added it to my lib folder. This too didn't help. So how can I fix this error?
UPDATE
full stacktrace
SEVERE: Error configuring application listener of class
com.sun.xmk.ws.transport.http.servlet.WSServletContextListener
java.lang.ClassNotFoundException: com.sun.xmk.ws.transport.http.servlet.WSServletContextListener
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1714)
at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1559)
at org.apache.catalina.core.DefaultInstanceManager.loadClass(DefaultInstanceManager.java:532)
at org.apache.catalina.core.DefaultInstanceManager.loadClassMaybePrivileged(DefaultInstanceManager.java:514)
at org.apache.catalina.core.DefaultInstanceManager.newInstance(DefaultInstanceManager.java:133)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4727)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5285)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:633)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:977)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1655)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

Instead of putting the jars in your app's WEB-INF/lib dir, put it under the lib dir under Tomcat install directory. That should fix the error.