Develop Reference

NoSuchFileException: /usr/share/java/etc/webdefault.xml when running jetty 9 server in Intellij

My computer is:
Debian Buster
jetty-9.4.15.v20190215
openjdk 11.0.7 2020-04-14
OpenJDK Runtime Environment (build 11.0.7+10-post-Debian-3deb10u1)
OpenJDK 64-Bit Server VM (build 11.0.7+10-post-Debian-3deb10u1, mixed mode, sharing)
IntelliJ IDEA 2020.1.1 (Ultimate Edition)
Build #IU-201.7223.91, built on April 30, 2020
I installed jetty server by a command sudo apt install jetty9. I created a simple hello world web application as in a tutorial: https://www.jetbrains.com/help/idea/creating-and-running-your-first-java-ee-application.html
I configured the project to run with jetty server. Each time I press run the exception java.nio.file.NoSuchFileException: /usr/share/java/etc/webdefault.xml appears.
This is the log:
/usr/lib/jvm/java-1.11.0-openjdk-amd64/bin/java -DSTOP.PORT=0 -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=1099 -Dcom.sun.management.jmxremote.password.file=/home/u/.cache/JetBrains/IntelliJIdea2020.1/jetty/Jetty_9_4_15_v20190215_First-java-ee-application/jmxremote.password -Dcom.sun.management.jmxremote.access.file=/home/u/.cache/JetBrains/IntelliJIdea2020.1/jetty/Jetty_9_4_15_v20190215_First-java-ee-application/jmxremote.access -Dcom.sun.management.jmxremote.ssl=false -DOPTIONS=jmx -javaagent:/opt/idea-IU-201.7223.91/lib/idea_rt.jar=35455:/opt/idea-IU-201.7223.91/bin -Dfile.encoding=UTF-8 -classpath /usr/share/jetty9/start.jar org.eclipse.jetty.start.Main --module=jmx /tmp/context2config/jetty-contexts.xml
Detected server http port: 8080
[2020-06-04 11:19:21,720] Artifact First-java-ee-application:war exploded: Waiting for server connection to start artifact deployment...
2020-06-04 23:19:22.847:INFO::main: Logging initialized #1174ms to org.eclipse.jetty.util.log.StdErrLog
2020-06-04 23:19:23.028:WARN:oejx.XmlConfiguration:main: Property 'threads.min' is deprecated, use 'jetty.threadPool.minThreads' instead
2020-06-04 23:19:23.030:WARN:oejx.XmlConfiguration:main: Property 'threads.max' is deprecated, use 'jetty.threadPool.maxThreads' instead
2020-06-04 23:19:23.032:WARN:oejx.XmlConfiguration:main: Property 'threads.timeout' is deprecated, use 'jetty.threadPool.idleTimeout' instead
2020-06-04 23:19:23.234:WARN:oejx.XmlConfiguration:main: Property 'jetty.port' is deprecated, use 'jetty.http.port' instead
2020-06-04 23:19:23.234:WARN:oejx.XmlConfiguration:main: Property 'http.timeout' is deprecated, use 'jetty.http.idleTimeout' instead
STOP.PORT=33549
STOP.KEY=19labqkc4txq8
2020-06-04 23:19:23.355:INFO:oejs.Server:main: jetty-9.4.15.v20190215; built: unknown; git: unknown; jvm 11.0.7+10-post-Debian-3deb10u1
2020-06-04 23:19:23.390:INFO:oejdp.ScanningAppProvider:main: Deployment monitor [file:///var/lib/jetty9/webapps/] at interval 1
2020-06-04 23:19:23.495:WARN:oejw.WebAppContext:main: Failed startup of context o.e.j.w.WebAppContext#273444fe{root,/,file:///var/lib/jetty9/webapps/root/,UNAVAILABLE}{/root}
java.nio.file.NoSuchFileException: /usr/share/java/etc/webdefault.xml
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:219)
at java.base/java.nio.file.Files.newByteChannel(Files.java:370)
at java.base/java.nio.file.Files.newByteChannel(Files.java:421)
at java.base/java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:420)
at java.base/java.nio.file.Files.newInputStream(Files.java:155)
at org.eclipse.jetty.util.resource.PathResource.getInputStream(PathResource.java:394)
at org.eclipse.jetty.webapp.Descriptor.parse(Descriptor.java:55)
at org.eclipse.jetty.webapp.WebDescriptor.parse(WebDescriptor.java:212)
at org.eclipse.jetty.webapp.MetaData.setDefaults(MetaData.java:168)
at org.eclipse.jetty.webapp.WebXmlConfiguration.preConfigure(WebXmlConfiguration.java:53)
at org.eclipse.jetty.webapp.WebAppContext.preConfigure(WebAppContext.java:506)
at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:544)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at org.eclipse.jetty.deploy.bindings.StandardStarter.processBinding(StandardStarter.java:46)
at org.eclipse.jetty.deploy.AppLifeCycle.runBindings(AppLifeCycle.java:192)
at org.eclipse.jetty.deploy.DeploymentManager.requestAppGoal(DeploymentManager.java:505)
at org.eclipse.jetty.deploy.DeploymentManager.addApp(DeploymentManager.java:151)
at org.eclipse.jetty.deploy.providers.ScanningAppProvider.fileAdded(ScanningAppProvider.java:180)
at org.eclipse.jetty.deploy.providers.WebAppProvider.fileAdded(WebAppProvider.java:432)
at org.eclipse.jetty.deploy.providers.ScanningAppProvider$1.fileAdded(ScanningAppProvider.java:64)
at org.eclipse.jetty.util.Scanner.reportAddition(Scanner.java:610)
at org.eclipse.jetty.util.Scanner.reportDifferences(Scanner.java:529)
at org.eclipse.jetty.util.Scanner.scan(Scanner.java:392)
at org.eclipse.jetty.util.Scanner.doStart(Scanner.java:313)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at org.eclipse.jetty.deploy.providers.ScanningAppProvider.doStart(ScanningAppProvider.java:150)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at org.eclipse.jetty.deploy.DeploymentManager.startAppProvider(DeploymentManager.java:579)
at org.eclipse.jetty.deploy.DeploymentManager.doStart(DeploymentManager.java:240)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at org.eclipse.jetty.util.component.ContainerLifeCycle.start(ContainerLifeCycle.java:138)
at org.eclipse.jetty.server.Server.start(Server.java:415)
at org.eclipse.jetty.util.component.ContainerLifeCycle.doStart(ContainerLifeCycle.java:117)
at org.eclipse.jetty.server.handler.AbstractHandler.doStart(AbstractHandler.java:113)
at org.eclipse.jetty.server.Server.doStart(Server.java:382)
at org.eclipse.jetty.util.component.AbstractLifeCycle.start(AbstractLifeCycle.java:68)
at org.eclipse.jetty.xml.XmlConfiguration$1.run(XmlConfiguration.java:1572)
at org.eclipse.jetty.xml.XmlConfiguration$1.run(XmlConfiguration.java:1512)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.jetty.xml.XmlConfiguration.main(XmlConfiguration.java:1511)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.eclipse.jetty.start.Main.invokeMain(Main.java:220)
at org.eclipse.jetty.start.Main.start(Main.java:490)
at org.eclipse.jetty.start.Main.main(Main.java:77)
2020-06-04 23:19:23.507:INFO:oejdp.ScanningAppProvider:main: Deployment monitor [file:///tmp/context2deploy/] at interval 1
Connected to server
[2020-06-04 11:19:23,548] Artifact First-java-ee-application:war exploded: Artifact is being deployed, please wait...
2020-06-04 23:19:23.544:INFO:oejs.AbstractConnector:main: Started ServerConnector#37d4349f{HTTP/1.1,[http/1.1]}{0.0.0.0:8080}
2020-06-04 23:19:23.544:INFO:oejs.Server:main: Started #1872ms
2020-06-04 23:19:23.679:INFO:oejsh.ContextHandler:RMI TCP Connection(2)-127.0.0.1: Stopped o.e.j.w.WebAppContext#273444fe{root,/,null,UNAVAILABLE}{/root}
2020-06-04 23:19:25.664:INFO:oeja.AnnotationConfiguration:Scanner-1: Scanning elapsed time=0ms
2020-06-04 23:19:25.755:INFO:oejshC.ROOT:Scanner-1: Warning: No org.apache.tomcat.JarScanner set in ServletContext. Falling back to default JarScanner implementation.
2020-06-04 23:19:25.850:INFO:oajs.TldScanner:Scanner-1: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
2020-06-04 23:19:25.861:INFO:oejs.session:Scanner-1: DefaultSessionIdManager workerName=node0
2020-06-04 23:19:25.861:INFO:oejs.session:Scanner-1: No SessionScavenger set, using defaults
2020-06-04 23:19:25.862:INFO:oejs.session:Scanner-1: node0 Scavenging every 660000ms
2020-06-04 23:19:25.893:INFO:oejsh.ContextHandler:Scanner-1: Started o.e.j.w.WebAppContext#7850add7{/,file:///home/u/Dropbox/IdeaProjects/First-java-ee-application/out/artifacts/First_java_ee_application_war_exploded/,AVAILABLE}
[2020-06-04 11:19:26,386] Artifact First-java-ee-application:war exploded: Artifact is deployed successfully
[2020-06-04 11:19:26,387] Artifact First-java-ee-application:war exploded: Deploy took 2,838 milliseconds
2020-06-04 23:19:27.388:WARN:oejs.session:qtp990355670-23: Problem checking if id F8AC12E18F0A088B1D85F8D275A4B947 is in use java.lang.NullPointerException
How to fix it?

wso2 app server (carbon) startup error

I am trying to start up the WSO2 app server and get this error. I have nothing deployed except I set up some data services. It was working fine and now it gives this error. I am on Windows 8.1 and running Java 1.7.0_75. I thought I read somewhere about a setup.conf file being corrupted but can't find that article of this file anymore. I do have Java 1.8 on my machine but disabled that in windows and also made sure the java_home is set correctly. Thanks for your help in advance.
[2015-07-06 10:12:19,672] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Starting WSO2 Carbon...
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Operating System : Windows 8.1 6.3, amd64
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Java Home : D:\Java\jdk1.7.0_75\jre
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Java Version : 1.7.0_75
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Java VM : Java HotSpot(TM) 64-Bit Server VM 24.75-b04,Oracle Corporation
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Carbon Home : D:/development/wso2as-5.2.1
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - Java Temp Dir : D:/development/wso2as-5.2.1/tmp
[2015-07-06 10:12:19,680] INFO {org.wso2.carbon.core.internal.CarbonCoreActivator} - User : Dean, en-US, America/New_York
[2015-07-06 10:12:19,752] WARN {org.wso2.carbon.core.bootup.validator.util.ValidationResultPrinter} - The running OS : Windows 8.1 is not a tested Operating System for running WSO2 Carbon
[2015-07-06 10:12:19,752] WARN {org.wso2.carbon.core.bootup.validator.util.ValidationResultPrinter} - The default keystore (wso2carbon.jks) is currently being used. To maximize security when deploying to a production environment, configure a new keystore with a unique password in the production server profile.
[2015-07-06 10:12:19,800] INFO {org.wso2.carbon.databridge.agent.thrift.AgentHolder} - Agent created !
[2015-07-06 10:12:19,816] INFO {org.wso2.carbon.databridge.agent.thrift.internal.AgentDS} - Successfully deployed Agent Client
[2015-07-06 10:12:21,048] INFO {org.wso2.carbon.registry.core.jdbc.EmbeddedRegistryService} - Configured Registry in 43ms
[2015-07-06 10:12:21,110] INFO {org.wso2.carbon.registry.core.internal.RegistryCoreServiceComponent} - Registry Mode : READ-WRITE
[2015-07-06 10:12:21,918] INFO {org.wso2.carbon.user.core.internal.UserStoreMgtDSComponent} - Carbon UserStoreMgtDSComponent activated successfully.
[2015-07-06 10:12:30,565] FATAL {org.wso2.carbon.core.init.CarbonServerManager} - WSO2 Carbon initialization Failed
org.apache.axiom.om.OMException: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[31,21]
Message: Invalid byte 1 of 1-byte UTF-8 sequence.
at org.apache.axiom.om.impl.builder.StAXOMBuilder.next(StAXOMBuilder.java:296)
at org.apache.axiom.om.impl.llom.OMSerializableImpl.build(OMSerializableImpl.java:78)
at org.apache.axiom.om.impl.llom.OMElementImpl.build(OMElementImpl.java:722)
at org.apache.axis2.util.XMLUtils.toOM(XMLUtils.java:595)
at org.apache.axis2.util.XMLUtils.toOM(XMLUtils.java:575)
at org.apache.axis2.deployment.DescriptionBuilder.buildOM(DescriptionBuilder.java:97)
at org.apache.axis2.deployment.AxisConfigBuilder.populateConfig(AxisConfigBuilder.java:91)
at org.wso2.carbon.core.CarbonAxisConfigurator.populateAxisConfiguration(CarbonAxisConfigurator.java:308)
at org.wso2.carbon.core.CarbonAxisConfigurator.getAxisConfiguration(CarbonAxisConfigurator.java:188)
at org.apache.axis2.context.ConfigurationContextFactory.createConfigurationContext(ConfigurationContextFactory.java:64)
at org.wso2.carbon.core.CarbonConfigurationContextFactory.createNewConfigurationContext(CarbonConfigurationContextFactory.java:65)
at org.wso2.carbon.core.init.CarbonServerManager.initializeCarbon(CarbonServerManager.java:398)
at org.wso2.carbon.core.init.CarbonServerManager.start(CarbonServerManager.java:219)
at org.wso2.carbon.core.internal.CarbonCoreServiceComponent.activate(CarbonCoreServiceComponent.java:77)
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.eclipse.equinox.internal.ds.model.ServiceComponent.activate(ServiceComponent.java:260)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.activate(ServiceComponentProp.java:146)
at org.eclipse.equinox.internal.ds.model.ServiceComponentProp.build(ServiceComponentProp.java:347)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponent(InstanceProcess.java:620)
at org.eclipse.equinox.internal.ds.InstanceProcess.buildComponents(InstanceProcess.java:197)
at org.eclipse.equinox.internal.ds.Resolver.getEligible(Resolver.java:343)
at org.eclipse.equinox.internal.ds.SCRManager.serviceChanged(SCRManager.java:222)
at org.eclipse.osgi.internal.serviceregistry.FilteredServiceListener.serviceChanged(FilteredServiceListener.java:107)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.dispatchEvent(BundleContextImpl.java:861)
at org.eclipse.osgi.framework.eventmgr.EventManager.dispatchEvent(EventManager.java:230)
at org.eclipse.osgi.framework.eventmgr.ListenerQueue.dispatchEventSynchronous(ListenerQueue.java:148)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEventPrivileged(ServiceRegistry.java:819)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.publishServiceEvent(ServiceRegistry.java:771)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.register(ServiceRegistrationImpl.java:130)
at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.registerService(ServiceRegistry.java:214)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.registerService(BundleContextImpl.java:433)
at org.eclipse.equinox.http.servlet.internal.Activator.registerHttpService(Activator.java:81)
at org.eclipse.equinox.http.servlet.internal.Activator.addProxyServlet(Activator.java:60)
at org.eclipse.equinox.http.servlet.internal.ProxyServlet.init(ProxyServlet.java:40)
at org.wso2.carbon.tomcat.ext.servlet.DelegationServlet.init(DelegationServlet.java:38)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1284)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1197)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1087)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5229)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5516)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1575)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1565)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
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: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[31,21]
Message: Invalid byte 1 of 1-byte UTF-8 sequence.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:596)
at org.apache.axiom.util.stax.wrapper.XMLStreamReaderWrapper.next(XMLStreamReaderWrapper.java:225)
at org.apache.axiom.util.stax.dialect.SJSXPStreamReaderWrapper.next(SJSXPStreamReaderWrapper.java:138)
at org.apache.axiom.om.impl.builder.StAXOMBuilder.parserNext(StAXOMBuilder.java:681)
at org.apache.axiom.om.impl.builder.StAXOMBuilder.next(StAXOMBuilder.java:214)
... 49 more
Carbon Server WSO2 Carbon 4.2 based server at localhost is shutting down...
Carbon Server WSO2 Carbon 4.2 based server at localhost has shutted down...

It looks like /repository/conf/axis2/axis2.xml has a non-compatible character, most probably at the line mentioned.

GAE - ClassNotFoundException after deployment to Appspot server

I've got the Google's example Guestbook project created using Maven's archetype com.google.appengine.archetypes:guestbook-archetype. When I run it locally using mvn appengine:devserver it works alright, the problems start when I try to deploy it on Google's Appspot. I get the following message:
Error: Server Error
The server encountered an error and could not complete your request.
If the problem persists, please report your problem and mention this error message and the query that caused it.
In the logs I can see this:
2013-05-01 05:38:28.356 / 500 3166ms 0kb Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
2001:6d8:10:a014:5176:bdbe:c152:53c0 - - [01/May/2013:05:38:28 -0700] "GET / HTTP/1.1" 500 0 - "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31" "aghinzop.appspot.com" ms=3167 cpu_ms=2100 loading_request=1 app_engine_release=1.7.7 instance=00c61b117cdf51947e909cbfaf52e1739a7f4c
W 2013-05-01 05:38:28.325
EXCEPTION
java.lang.ClassNotFoundException: ioserv.ioserv.SignGuestbookServlet
at com.google.appengine.runtime.Request.process-53e8711216f37199(Request.java)
at java.lang.ClassLoader.loadClass(ClassLoader.java:359)
at org.mortbay.util.Loader.loadClass(Loader.java:91)
at org.mortbay.util.Loader.loadClass(Loader.java:71)
at org.mortbay.jetty.servlet.Holder.doStart(Holder.java:73)
at org.mortbay.jetty.servlet.ServletHolder.doStart(ServletHolder.java:242)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at org.mortbay.jetty.servlet.ServletHandler.initialize(ServletHandler.java:685)
at org.mortbay.jetty.servlet.Context.startContext(Context.java:140)
at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250)
at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517)
at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:480)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:487)
at com.google.tracing.TraceContext.runInContext(TraceContext.java:774)
at com.google.tracing.TraceContext$DoInTraceContext.runInContext(TraceContext.java:751)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:342)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:334)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:484)
at java.lang.Thread.run(Thread.java:722)
E 2013-05-01 05:38:28.326
javax.servlet.ServletContext log: unavailable
javax.servlet.UnavailableException: ioserv.ioserv.SignGuestbookServlet
at org.mortbay.jetty.servlet.Holder.doStart(Holder.java:79)
at org.mortbay.jetty.servlet.ServletHolder.doStart(ServletHolder.java:242)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at org.mortbay.jetty.servlet.ServletHandler.initialize(ServletHandler.java:685)
at org.mortbay.jetty.servlet.Context.startContext(Context.java:140)
at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250)
at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517)
at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.createHandler(AppVersionHandlerMap.java:219)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.getHandler(AppVersionHandlerMap.java:194)
at com.google.apphosting.runtime.jetty.JettyServletEngineAdapter.serviceRequest(JettyServletEngineAdapter.java:134)
at com.google.apphosting.runtime.JavaRuntime$RequestRunnable.run(JavaRuntime.java:438)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:480)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:487)
at com.google.tracing.TraceContext.runInContext(TraceContext.java:774)
at com.google.tracing.TraceContext$DoInTraceContext.runInContext(TraceContext.java:751)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:342)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:334)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:484)
at com.google.apphosting.runtime.ThreadGroupPool$PoolEntry.run(ThreadGroupPool.java:251)
at java.lang.Thread.run(Thread.java:722)
W 2013-05-01 05:38:28.338
Failed startup of context com.google.apphosting.utils.jetty.RuntimeAppEngineWebAppContext#11c3e97{/,/base/data/home/apps/s~aghinzop/1.367061823227494749}
java.lang.NullPointerException
at java.lang.Class.isAssignableFrom(Native Method)
at org.mortbay.jetty.servlet.ServletHolder.doStart(ServletHolder.java:256)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at org.mortbay.jetty.servlet.ServletHandler.initialize(ServletHandler.java:685)
at org.mortbay.jetty.servlet.Context.startContext(Context.java:140)
at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250)
at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517)
at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.createHandler(AppVersionHandlerMap.java:219)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.getHandler(AppVersionHandlerMap.java:194)
at com.google.apphosting.runtime.jetty.JettyServletEngineAdapter.serviceRequest(JettyServletEngineAdapter.java:134)
at com.google.apphosting.runtime.JavaRuntime$RequestRunnable.run(JavaRuntime.java:438)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:480)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:487)
at com.google.tracing.TraceContext.runInContext(TraceContext.java:774)
at com.google.tracing.TraceContext$DoInTraceContext.runInContext(TraceContext.java:751)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:342)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:334)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:484)
at com.google.apphosting.runtime.ThreadGroupPool$PoolEntry.run(ThreadGroupPool.java:251)
at java.lang.Thread.run(Thread.java:722)
C 2013-05-01 05:38:28.342
Uncaught exception from servlet
javax.servlet.UnavailableException: Initialization failed.
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.createHandler(AppVersionHandlerMap.java:228)
at com.google.apphosting.runtime.jetty.AppVersionHandlerMap.getHandler(AppVersionHandlerMap.java:194)
at com.google.apphosting.runtime.jetty.JettyServletEngineAdapter.serviceRequest(JettyServletEngineAdapter.java:134)
at com.google.apphosting.runtime.JavaRuntime$RequestRunnable.run(JavaRuntime.java:438)
at com.google.tracing.TraceContext$TraceContextRunnable.runInContext(TraceContext.java:480)
at com.google.tracing.TraceContext$TraceContextRunnable$1.run(TraceContext.java:487)
at com.google.tracing.TraceContext.runInContext(TraceContext.java:774)
at com.google.tracing.TraceContext$DoInTraceContext.runInContext(TraceContext.java:751)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContextNoUnref(TraceContext.java:342)
at com.google.tracing.TraceContext$AbstractTraceContextCallback.runInInheritedContext(TraceContext.java:334)
at com.google.tracing.TraceContext$TraceContextRunnable.run(TraceContext.java:484)
at com.google.apphosting.runtime.ThreadGroupPool$PoolEntry.run(ThreadGroupPool.java:251)
at java.lang.Thread.run(Thread.java:722)
I 2013-05-01 05:38:28.355
This request caused a new process to be started for your application, and thus caused your application code to be loaded for the first time. This request may thus take longer and use more CPU than a typical request for your application.
Here are the basic settings I have in Eclipse and the deployment log (I use App Engine Eclipse Plugin).
I'm not sure what "disabled because this is a Maven project" means here. Could you explain? And should I check this box?
The App Engine SDK selected here is the one provided by the Eclipse Plugin.
Here are the libs provided by plugin. There are also some Maven libs added by the archetype.
And here are the libs in WEB-INF/lib. I can see that there are very few of them and I realize that something may be missing. The problem is when I try to copy libs into this folder I get Cannot paste the clipboard contents into the selected elements. How can I do this? In a normal Dynamic Web Project (using this facet) it's as easy as Properties>Deployment Assembly>Add but here I have no clue how to do this.
I'd really appreciate your help! Thank you!

I'm not sure what "disabled because this is a Maven project" means here. Could you explain? And should I check this box?
There are two ways to manage your application (specifically web folder), one letting maven do it, and other letting google eclipse plugin do it. Since your application is built by maven, default assumption is your web app management is done by maven itself, so google eclipse plugin has disabled it by default.
unless you are not removing maven, it should be as it is.
Coming to error, my guess is, though you are building and testing through maven, you might be trying to deploy through eclipse, please try mvn appengine:update and it should work.
hope it helps.

How to use MySQL persistence manager with Jackrabbit standalone

I've been successfully using Apache Jackrabbit 2.4.3 and now 2.6.0 (standalone server in both cases) using the default configuration, so the repository is stored on the filesystem.
How can I make it connect to a MySQL back end instead? I don't need to worry about migration, just set it up as a fresh install.
After trying the steps below, Jackrabbit fails to start correctly or populate the DATASTORE table in the database, and I find this error in the logs:
ERROR [main] RepositoryImpl.java:366 failed to start Repository: Cannot instantiate persistence manager org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager
javax.jcr.RepositoryException: Cannot instantiate persistence manager org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager
[... oodles of backtrace cut ...]
[edit: here's the full backtrace]
2013-03-04 10:59:27.526 WARN [main] Slf4jLog.java:89 unavailable
javax.jcr.RepositoryException: Cannot instantiate persistence manager org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager
at org.apache.jackrabbit.core.RepositoryImpl.createPersistenceManager(RepositoryImpl.java:1353) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.RepositoryImpl.createVersionManager(RepositoryImpl.java:486) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.RepositoryImpl.<init>(RepositoryImpl.java:311) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.RepositoryImpl.create(RepositoryImpl.java:589) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.RepositoryContext.create(RepositoryContext.java:149) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.servlet.jackrabbit.JackrabbitRepositoryServlet.init(JackrabbitRepositoryServlet.java:109) ~[jackrabbit-standalone-2.6.0.jar:na]
at javax.servlet.GenericServlet.init(GenericServlet.java:241) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.servlet.ServletHolder.initServlet(ServletHolder.java:440) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.servlet.ServletHolder.doStart(ServletHolder.java:263) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.servlet.ServletHandler.initialize(ServletHandler.java:685) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.servlet.Context.startContext(Context.java:140) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.handler.RequestLogHandler.doStart(RequestLogHandler.java:115) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.jetty.Server.doStart(Server.java:224) [jackrabbit-standalone-2.6.0.jar:na]
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50) [jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.standalone.Main.run(Main.java:173) [jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.standalone.Main.main(Main.java:60) [jackrabbit-standalone-2.6.0.jar:na]
Caused by: javax.jcr.RepositoryException: Could not load JDBC driver class org.gjt.mm.mysql.Driver
at org.apache.jackrabbit.core.util.db.ConnectionFactory.getDriverClass(ConnectionFactory.java:265) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.util.db.ConnectionFactory.createDataSource(ConnectionFactory.java:233) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.util.db.ConnectionFactory.getDataSource(ConnectionFactory.java:169) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.persistence.pool.BundleDbPersistenceManager.getDataSource(BundleDbPersistenceManager.java:569) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.persistence.pool.BundleDbPersistenceManager.init(BundleDbPersistenceManager.java:537) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager.init(MySqlPersistenceManager.java:51) ~[jackrabbit-standalone-2.6.0.jar:na]
at org.apache.jackrabbit.core.RepositoryImpl.createPersistenceManager(RepositoryImpl.java:1349) ~[jackrabbit-standalone-2.6.0.jar:na]
... 23 common frames omitted
Caused by: java.lang.ClassNotFoundException: org.gjt.mm.mysql.Driver
at java.net.URLClassLoader$1.run(URLClassLoader.java:217) ~[na:1.6.0_27]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.6.0_27]
at java.net.URLClassLoader.findClass(URLClassLoader.java:205) ~[na:1.6.0_27]
at java.lang.ClassLoader.loadClass(ClassLoader.java:321) ~[na:1.6.0_27]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) ~[na:1.6.0_27]
at java.lang.ClassLoader.loadClass(ClassLoader.java:266) ~[na:1.6.0_27]
at java.lang.Class.forName0(Native Method) ~[na:1.6.0_27]
at java.lang.Class.forName(Class.java:188) ~[na:1.6.0_27]
at org.apache.jackrabbit.core.util.db.ConnectionFactory.getDriverClass(ConnectionFactory.java:260) ~[jackrabbit-standalone-2.6.0.jar:na]
... 29 common frames omitted
What I've done so far:
I've created the Jackrabbit database/user, which I can connect to no problem:
mysql -D jackrabbit -u jackrabbit -h localhost -pjackrabbit
I started with a clean slate (empty /var/jackrabbit directory), except the configuration file comes from here: https://raw.github.com/wiki/jackalope/jackalope/files/repository.xml
Here's the startup script I'm using: https://github.com/sixty-nine/Jackrabbit-startup-script
And here's the java process that runs:
java -XX:MaxPermSize=128m -Xmx512M -Xms128M -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=1111 -Dcom.sun.management.jmxremote.authenticate=true -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.password.file=/opt/jackrabbit/startup/jmx.user -Dcom.sun.management.jmxremote.access.file=/opt/jackrabbit/startup/jmx.role -jar /opt/jackrabbit/jackrabbit-standalone-2.6.0.jar -h 127.0.0.1 -p 8080
I don't think I get far enough for it to matter, but I'm using MySQL 5.5.28-1.
I'm having the above problem with both 2.4.3 and 2.6.0.
Also:
java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.5) (6b24-1.11.5-1)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)
Plus I subsequently installed the MySQL JDBC library on Debian:
apt-get install libmysql-java

The MySqlPersistenceManager tries to load the driver class org.gjt.mm.mysql.Driver, which is very old. Try using a more recent driver class, the class com.mysql.jdbc.Driver instead. To do that, you would need to configure the persistence manager in the repository.xml and all workspace.xml files as follows:
<PersistenceManager ...>
...
<param name="driver" value="com.mysql.jdbc.Driver"/>
</PersistenceManager>

In order to load the MySQL driver with Apache Jackrabbit-standalone. You will need to update the jackrabbit-stabndalone-x.x.x.jar in MANIFEST.MF.
Simply add a Class-Path statement to the bottom of the file such as:
Class-Path: lib/mysql-connector-java-5.1.25-bin.jar
I had the same problem as you and this was the only way I could get the MySQL driver class recognized.

Answering my own question, although it doesn't directly answer it:
Instead of trying to use the jackrabbit-standalone version, I've successfully got it running under Tomcat by following the instructions here:
https://github.com/jackalope/jackalope/wiki/Running-jackrabbit-in-tomcat-with-mysql
This gives me what I need; a working Jackrabbit instance that connects to a MySQL data store. Although this doesn't help anyone who comes across this and specifically needs to use Jackrabbit standalone, I would say that setting it up under Tomcat proved much easier for me, so is worth considering.

Please do the following activities.
Un-jar the standalone server jar (in my case it is : jackrabbit-standalone-2.8.3). You will see many folders. among them you will find two folder. 1.com 2. org.
Un-jar mysql-connector-java-5.1.30-bin. again you will find above mentioned two folders. go inside both the folders and copy the git(org) and mysql(com)
Paste inside the step 1's folder respectively. and restart the standalone server.
Regards,
Nitesh

Logging.LogFactory error in google web application engine project developmenter

I am using the google web application engine and develop a project. I meet with a problem of runtime error like that :
Apr 28, 2011 10:28:36 AM com.google.apphosting.utils.jetty.JettyLogger warn
WARNING: Error starting handlers
java.lang.NoClassDefFoundError: org.apache.commons.logging.LogFactory is a restricted class. Please see the Google App Engine developer's guide for more details.
at com.google.appengine.tools.development.agent.runtime.Runtime.reject(Runtime.java:51)
at org.springframework.web.context.ContextLoader.<clinit>(ContextLoader.java:146)
at org.springframework.web.context.ContextLoaderListener.createContextLoader(ContextLoaderListener.java:53)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:44)
at org.mortbay.jetty.handler.ContextHandler.startContext(ContextHandler.java:548)
at org.mortbay.jetty.servlet.Context.startContext(Context.java:136)
at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250)
at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517)
at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130)
at org.mortbay.jetty.Server.doStart(Server.java:224)
at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
at com.google.appengine.tools.development.JettyContainerService.startContainer(JettyContainerService.java:185)
at com.google.appengine.tools.development.AbstractContainerService.startup(AbstractContainerService.java:147)
at com.google.appengine.tools.development.DevAppServerImpl.start(DevAppServerImpl.java:219)
at com.google.appengine.tools.development.DevAppServerMain$StartAction.apply(DevAppServerMain.java:164)
at com.google.appengine.tools.util.Parser$ParseResult.applyArgs(Parser.java:48)
at com.google.appengine.tools.development.DevAppServerMain.<init>(DevAppServerMain.java:113)
at com.google.appengine.tools.development.DevAppServerMain.main(DevAppServerMain.java:89)
Apr 28, 2011 10:28:36 AM com.google.apphosting.utils.jetty.JettyLogger debug
How can I get the solution for this?
Here is my logging.properties...
A default java.util.logging configuration.
(All App Engine logging is through java.util.logging by default).
#
To use this configuration, copy it into your application's WEB-INF
folder and add the following to your appengine-web.xml:
#
Set the default logging level for all loggers to WARNING
.level = ALL
handlers = java.util.logging.ConsoleHandler
java.util.logging.ConsoleHandler.level=ALL
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
Set the default logging level for ORM, specifically, to WARNING
DataNucleus.JDO.level=WARNING
DataNucleus.Persistence.level=WARNING
DataNucleus.Cache.level=WARNING
DataNucleus.MetaData.level=WARNING
DataNucleus.General.level=WARNING
DataNucleus.Utility.level=WARNING
DataNucleus.Transaction.level=WARNING
DataNucleus.Datastore.level=WARNING
DataNucleus.ClassLoading.level=WARNING
DataNucleus.Plugin.level=WARNING
DataNucleus.ValueGeneration.level=WARNING
DataNucleus.Enhancer.level=WARNING
DataNucleus.SchemaTool.level=WARNING
java.sql.level=INFO

It is possible you're missing commons-logging-xxx.jar in your build path