LMS

First Bug:
[13/02/2013 09:52:30,518] [Application-Thread] INFO com.lobeo.lms.core.CoreServiceListener - ServiceEvent: The service {com.lobeo.lms.framework.DeployerProcessor}={item.types=[war], service.access.group=Administrator, service.id=51} has been registered
[13/02/2013 09:52:30,518] [Application-Thread] INFO com.lobeo.lms.http.HttpServerActivator - Registering the http server service
[13/02/2013 09:52:30,518] [Application-Thread] INFO com.lobeo.lms.http.tomcat.TomcatHttpServerService - Creating the http server service for tomcat
[13/02/2013 09:52:30,533] [Application-Thread] INFO com.lobeo.lms.core.service.ServiceRegistry$Service - Creating a new service [com.lobeo.lms.http.service.HttpServerService]
[13/02/2013 09:52:30,533] [Application-Thread] INFO com.lobeo.lms.core.service.impl.ServiceRegistryImpl - Registering the service [Service-0:com.lobeo.lms.http.service.HttpServerService/HttpServer]
[13/02/2013 09:52:30,533] [Application-Thread] INFO com.lobeo.lms.core.CoreServiceListener - ServiceEvent: The service {com.lobeo.lms.http.service.HttpServerService}={service.access.group=Administrator, service.id=52} has been registered
[13/02/2013 09:52:30,533] [Application-Thread] INFO com.lobeo.lms.http.tomcat.TomcatServer - Configuring the tomcat http server
[13/02/2013 09:52:36,011] [Application-Thread] INFO com.lobeo.lms.http.tomcat.TomcatServer - Starting up the embedded server
[13/02/2013 09:52:49,397] [Application-Thread] INFO org.apache.catalina.core.AprLifecycleListener - The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: C:\Program Files\Java\jdk1.7.0_07\bin;C:\windows\Sun\Java\bin;C:\windows\system32;C:\windows;C:\Program Files\Common Files\Microsoft Shared\Windows Live;C:\Program Files (x86)\Common Files\Microsoft Shared\Windows Live;C:\windows\system32;C:\windows;C:\windows\System32\Wbem;C:\windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\WIDCOMM\Bluetooth Software\;C:\Program Files\WIDCOMM\Bluetooth Software\syswow64;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files (x86)\QuickTime\QTSystem\;C:\Program Files\TortoiseSVN\bin;C:\Program Files\apache-ant-1.8.4\bin;C:\Program Files\Java\jdk1.7.0_07\bin;.
[13/02/2013 09:53:00,632] [Application-Thread] INFO org.apache.coyote.http11.Http11NioProtocol - Initializing ProtocolHandler ["http-nio-8080"]
[13/02/2013 09:53:03,797] [Application-Thread] INFO org.apache.tomcat.util.net.NioSelectorPool - Using a shared selector for servlet write/read
[13/02/2013 09:53:03,802] [Application-Thread] INFO org.apache.coyote.ajp.AjpProtocol - Initializing ProtocolHandler ["ajp-bio-8009"]
[13/02/2013 09:53:03,817] [Application-Thread] INFO org.apache.catalina.startup.Catalina - Initialization processed in 27792 ms
[13/02/2013 09:53:04,419] [Application-Thread] INFO org.apache.catalina.core.StandardService - Starting service LMS
[13/02/2013 09:53:04,419] [Application-Thread] INFO org.apache.catalina.core.StandardEngine - Starting Servlet Engine: Apache Tomcat/7.0.23
[13/02/2013 09:53:04,949] [pool-2-thread-1] INFO org.apache.catalina.startup.HostConfig - Deploying web application directory C:\Users\Andrej\Lobeo\Eden\repo-system\HttpServer\webapps\WebToolkit~WTKBrowserConnector
[13/02/2013 09:53:05,934] [pool-2-thread-1] INFO org.apache.catalina.loader.WebappLoader - Dual registration of jndi stream handler: factory already defined
[13/02/2013 09:53:06,205] [pool-2-thread-1] INFO org.apache.catalina.loader.WebappLoader - Unknown loader org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader@1414f5dc class org.eclipse.osgi.internal.baseadaptor.DefaultClassLoader
[13/02/2013 09:53:06,790] [pool-2-thread-1] ERROR org.apache.catalina.startup.ContextConfig - Unable to process JNDI URL [jndi:/localhost/WebToolkit/WTKBrowserConnector/WEB-INF/classes] for annotations
java.net.MalformedURLException: unknown protocol: jndi
at java.net.URL.<init>(URL.java:590)
at java.net.URL.<init>(URL.java:480)
at java.net.URL.<init>(URL.java:429)
at org.apache.catalina.startup.ContextConfig.processAnnotationsJndi(ContextConfig.java:1886)
at org.apache.catalina.startup.ContextConfig.processAnnotationsUrl(ContextConfig.java:1810)
at org.apache.catalina.startup.ContextConfig.webConfig(ContextConfig.java:1203)
at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:828)
at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:302)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5148)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:866)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:842)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:615)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1095)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1617)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
at java.lang.Thread.run(Thread.java:722)
[13/02/2013 09:53:07,550] [pool-2-thread-1] INFO com.lobeo.lms.http.servlet.LoginServlet - Initializing the LoginServlet
[13/02/2013 09:53:07,550] [pool-2-thread-1] INFO com.lobeo.lms.http.servlet.LoginServlet - Loading the login page Login.html
[13/02/2013 09:53:07,945] [pool-2-thread-1] INFO com.lobeo.lms.http.servlet.ErrorServlet - Initializing the error servlet
[13/02/2013 09:53:07,945] [pool-2-thread-1] INFO com.lobeo.lms.http.servlet.ErrorServlet - Loading the sign in page Error.html
[13/02/2013 09:53:08,055] [Application-Thread] INFO org.apache.coyote.http11.Http11NioProtocol - Starting ProtocolHandler ["http-nio-8080"]
[13/02/2013 09:53:08,100] [Application-Thread] INFO org.apache.coyote.ajp.AjpProtocol - Starting ProtocolHandler ["ajp-bio-8009"]
[13/02/2013 09:53:08,105] [Application-Thread] INFO org.apache.catalina.startup.Catalina - Server startup in 4287 ms



Second Bug:
[13/02/2013 09:53:28,554] [Application-Thread] INFO com.lobeo.lms.core.CoreBundleListener - BundleEvent: The OSGi bundle com.lobeo.lms.WebToolkit.jar has been uninstalled
[13/02/2013 09:53:28,709] [Application-Thread] ERROR com.lobeo.lms.module.ModuleRepository - Unable to process the module WebToolkit into the repository
java.io.IOException: An error occurred when starting the module WebToolkit
at com.lobeo.lms.module.ModuleRepository.startModule(ModuleRepository.java:420)
at com.lobeo.lms.module.ModuleRepository.processModuleDirectory(ModuleRepository.java:147)
at com.lobeo.lms.core.Application.run(Application.java:472)
Caused by: java.io.IOException: The context /WebToolkit/WTKBrowserConnector is already registered
at com.lobeo.lms.http.tomcat.TomcatServer.createContext(TomcatServer.java:305)
at com.lobeo.lms.http.tomcat.TomcatServer.deployApplication(TomcatServer.java:456)
at com.lobeo.lms.http.deployer.WarProcessor2.processItemStartup(WarProcessor2.java:351)
at com.lobeo.lms.module.deployer.DeployerImpl.startItem(DeployerImpl.java:244)
at com.lobeo.lms.module.ModuleRepository.startModule(ModuleRepository.java:383)
... 2 more
[13/02/2013 09:53:28,889] [Application-Thread] INFO com.lobeo.lms.module.ModuleRepository - Scan the module directory Administration
[13/02/2013 09:53:28,919] [Application-Thread] INFO com.lobeo.lms.module.Module - Create a new Module from the descriptor[C:\Users\Andrej\Lobeo\Eden\bin\..\repo-system\Administration\module.xml]
[13/02/2013 09:53:28,924] [Application-Thread] INFO com.lobeo.lms.module.Module - Binding the module descriptor of Administration with the module
[13/02/2013 09:53:29,409] [Application-Thread] INFO com.lobeo.lms.module.Module - Load module properties
[13/02/2013 09:53:29,409] [Application-Thread] INFO com.lobeo.lms.module.Module - Load items
[13/02/2013 09:53:29,409] [Application-Thread] INFO com.lobeo.lms.module.ModuleRepository - Registering the module Administration into repository repo-system
[13/02/2013 09:53:29,409] [Application-Thread] INFO com.lobeo.lms.module.ModuleRepository - Trying to start a module

Third Bug:
[13/02/2013 18:38:46,434] [Application-Thread] INFO com.lobeo.lms.core.CoreBundleListener - BundleEvent: The OSGi bundle com.lobeo.lms.WebToolkit.jar has been uninstalled
[13/02/2013 18:38:46,668] [Application-Thread] ERROR com.lobeo.lms.module.ModuleRepository - Unable to process the module WebToolkit into the repository
java.io.IOException: An error occurred when starting the module WebToolkit
at com.lobeo.lms.module.ModuleRepository.startModule(ModuleRepository.java:420)
at com.lobeo.lms.module.ModuleRepository.processModuleDirectory(ModuleRepository.java:147)
at com.lobeo.lms.core.Application.run(Application.java:472)
Caused by: org.osgi.framework.BundleException
at org.eclipse.osgi.framework.internal.core.Framework.installWorkerPrivileged(Framework.java:982)
at org.eclipse.osgi.framework.internal.core.Framework$1.run(Framework.java:838)
at org.eclipse.osgi.framework.internal.core.Framework$1.run(Framework.java:1)
at java.security.AccessController.doPrivileged(Native Method)
at org.eclipse.osgi.framework.internal.core.Framework.installWorker(Framework.java:897)
at org.eclipse.osgi.framework.internal.core.Framework.installBundle(Framework.java:833)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.installBundle(BundleContextImpl.java:137)
at org.eclipse.osgi.framework.internal.core.BundleContextImpl.installBundle(BundleContextImpl.java:131)
at com.lobeo.lms.http.deployer.WarProcessor2.processItemInstall(WarProcessor2.java:251)
at com.lobeo.lms.module.deployer.DeployerImpl.installItem(DeployerImpl.java:198)
at com.lobeo.lms.module.ModuleRepository.startModule(ModuleRepository.java:377)
... 2 more
Caused by: java.lang.NullPointerException
at com.lobeo.lms.hook.impl.LMSBundleFileWrapperFactoryHook.wrapBundleFile(LMSBundleFileWrapperFactoryHook.java:83)
at org.eclipse.osgi.internal.baseadaptor.BaseStorage.createBundleFile(BaseStorage.java:756)
at org.eclipse.osgi.baseadaptor.BaseAdaptor.createBundleFile(BaseAdaptor.java:486)
at org.eclipse.osgi.baseadaptor.BaseData.getBundleFile(BaseData.java:405)
at org.eclipse.osgi.baseadaptor.BaseData.getEntry0(BaseData.java:114)
at org.eclipse.osgi.baseadaptor.BaseData.getEntry(BaseData.java:105)
at org.eclipse.osgi.internal.baseadaptor.AdaptorUtil.loadManifestFrom(AdaptorUtil.java:187)
at org.eclipse.core.runtime.internal.adaptor.EclipseStorageHook.getGeneratedManifest0(EclipseStorageHook.java:410)
at org.eclipse.core.runtime.internal.adaptor.EclipseStorageHook.getGeneratedManifest(EclipseStorageHook.java:397)
at org.eclipse.core.runtime.internal.adaptor.EclipseStorageHook.createCachedManifest(EclipseStorageHook.java:392)
at org.eclipse.core.runtime.internal.adaptor.EclipseStorageHook.getManifest(EclipseStorageHook.java:512)
at org.eclipse.osgi.internal.baseadaptor.BaseStorage.loadManifest(BaseStorage.java:316)
at org.eclipse.osgi.internal.baseadaptor.BundleInstall.begin(BundleInstall.java:82)
at org.eclipse.osgi.framework.internal.core.Framework.installWorkerPrivileged(Framework.java:930)
... 12 more
[13/02/2013 18:38:46,683] [Application-Thread] INFO com.lobeo.lms.core.StdOut -