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qbicsoftware / projectbrowser-portlet

QBiC Project Browser enables users to browse and manage their projects. Further, users can run analysis pipelines on registered data.
MIT License
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Clicking on "Sample Notes" produces an exception #3

Closed chahuistle closed 6 years ago

chahuistle commented 6 years ago

Project > biological samples > extracted samples, click on a sample. Clicking on sampling notes produces the following exception in the log:

09.08.2018 14:48:32 [ERROR] [MultiscaleController] - Error parsing XML
javax.xml.bind.JAXBException: Provider com.sun.xml.internal.bind.v2.ContextFactory could not be instantiated: javax.xml.bind.JAXBException: "model.notes" doesnt contain ObjectFactory.class or jaxb.index
 - with linked exception:
[javax.xml.bind.JAXBException: "model.notes" doesnt contain ObjectFactory.class or jaxb.index]
    at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:146)
    at javax.xml.bind.ContextFinder.find(ContextFinder.java:356)
    at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:431)
    at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:394)
    at javax.xml.bind.JAXBContext.newInstance(JAXBContext.java:298)
    at life.qbic.projectbrowser.helpers.HistoryReader.parseNotes(HistoryReader.java:63)
    at life.qbic.projectbrowser.controllers.MultiscaleController.update(MultiscaleController.java:103)
    at life.qbic.projectbrowser.components.MultiscaleComponent.updateUI(MultiscaleComponent.java:75)
    at life.qbic.projectbrowser.views.SampleView.updateNoteComponent(SampleView.java:303)
    at life.qbic.projectbrowser.views.SampleView.updateContent(SampleView.java:213)
    at life.qbic.projectbrowser.views.SampleView.enter(SampleView.java:614)
    at com.vaadin.navigator.Navigator.navigateTo(Navigator.java:621)
    at com.vaadin.navigator.Navigator.navigateTo(Navigator.java:580)
    at life.qbic.projectbrowser.controllers.State.notifyObservers(State.java:45)
    at life.qbic.projectbrowser.components.BiologicalSamplesComponent$8.itemClick(BiologicalSamplesComponent.java:424)
    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.vaadin.event.ListenerMethod.receiveEvent(ListenerMethod.java:510)
    at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:200)
    at com.vaadin.event.EventRouter.fireEvent(EventRouter.java:163)
    at com.vaadin.server.AbstractClientConnector.fireEvent(AbstractClientConnector.java:1015)
    at com.vaadin.ui.Grid.access$1900(Grid.java:183)
    at com.vaadin.ui.Grid$3.itemClick(Grid.java:4792)
    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.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:158)
    at com.vaadin.server.ServerRpcManager.applyInvocation(ServerRpcManager.java:119)
    at com.vaadin.server.communication.ServerRpcHandler.handleInvocation(ServerRpcHandler.java:437)
    at com.vaadin.server.communication.ServerRpcHandler.handleInvocations(ServerRpcHandler.java:402)
    at com.vaadin.server.communication.ServerRpcHandler.handleRpc(ServerRpcHandler.java:273)
    at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:90)
    at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:41)
    at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1422)
    at com.vaadin.server.VaadinPortlet.handleRequest(VaadinPortlet.java:548)
    at com.vaadin.server.VaadinPortlet.serveResource(VaadinPortlet.java:631)
    at life.qbic.projectbrowser.helpers.CustomVaadinPortlet.serveResource(CustomVaadinPortlet.java:134)
    at com.liferay.portlet.FilterChainImpl.doFilter(FilterChainImpl.java:122)
    at com.liferay.portlet.ScriptDataPortletFilter.doFilter(ScriptDataPortletFilter.java:82)
    at com.liferay.portlet.FilterChainImpl.doFilter(FilterChainImpl.java:116)
    at com.liferay.portal.kernel.portlet.PortletFilterUtil.doFilter(PortletFilterUtil.java:71)
    at com.liferay.portal.kernel.servlet.PortletServlet.service(PortletServlet.java:112)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:116)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilter.doFilter(InvokerFilter.java:119)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
    at com.liferay.portlet.InvokerPortletImpl.invoke(InvokerPortletImpl.java:580)
    at com.liferay.portlet.InvokerPortletImpl.invokeResource(InvokerPortletImpl.java:675)
    at com.liferay.portlet.InvokerPortletImpl.serveResource(InvokerPortletImpl.java:441)
    at com.liferay.portlet.PortletContainerImpl._doServeResource(PortletContainerImpl.java:775)
    at com.liferay.portlet.PortletContainerImpl.serveResource(PortletContainerImpl.java:149)
    at com.liferay.portlet.SecurityPortletContainerWrapper.serveResource(SecurityPortletContainerWrapper.java:166)
    at com.liferay.portlet.RestrictPortletContainerWrapper.serveResource(RestrictPortletContainerWrapper.java:166)
    at com.liferay.portal.kernel.portlet.PortletContainerUtil.serveResource(PortletContainerUtil.java:164)
    at com.liferay.portal.action.LayoutAction.processLayout(LayoutAction.java:394)
    at com.liferay.portal.action.LayoutAction.doExecute(LayoutAction.java:200)
    at com.liferay.portal.action.LayoutAction.execute(LayoutAction.java:95)
    at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:431)
    at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:236)
    at com.liferay.portal.struts.PortalRequestProcessor.process(PortalRequestProcessor.java:168)
    at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1196)
    at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:432)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
    at com.liferay.portal.servlet.MainServlet.callParentService(MainServlet.java:557)
    at com.liferay.portal.servlet.MainServlet.service(MainServlet.java:534)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:116)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.uploadservletrequest.UploadServletRequestFilter.processFilter(UploadServletRequestFilter.java:93)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.secure.SecureFilter.processFilter(SecureFilter.java:308)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.jsoncontenttype.JSONContentTypeFilter.processFilter(JSONContentTypeFilter.java:42)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilter.doFilter(InvokerFilter.java:119)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:748)
    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:486)
    at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:411)
    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:338)
    at com.liferay.portal.servlet.FriendlyURLServlet.service(FriendlyURLServlet.java:161)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:116)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.uploadservletrequest.UploadServletRequestFilter.processFilter(UploadServletRequestFilter.java:93)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.gzip.GZipFilter.processFilter(GZipFilter.java:123)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.secure.SecureFilter.processFilter(SecureFilter.java:308)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.i18n.I18nFilter.processFilter(I18nFilter.java:254)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.etag.ETagFilter.processFilter(ETagFilter.java:86)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.jsoncontenttype.JSONContentTypeFilter.processFilter(JSONContentTypeFilter.java:42)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.autologin.AutoLoginFilter.processFilter(AutoLoginFilter.java:268)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.sso.ntlm.NtlmPostFilter.processFilter(NtlmPostFilter.java:83)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.sharepoint.SharepointFilter.processFilter(SharepointFilter.java:88)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.BaseFilter.processFilter(BaseFilter.java:169)
    at com.liferay.portal.servlet.filters.virtualhost.VirtualHostFilter.processFilter(VirtualHostFilter.java:226)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDirectCallFilter(InvokerFilterChain.java:185)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:96)
    at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:738)
    at com.liferay.portal.servlet.filters.urlrewrite.UrlRewriteFilter.processFilter(UrlRewriteFilter.java:57)
    at com.liferay.portal.kernel.servlet.BaseFilter.doFilter(BaseFilter.java:59)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDirectCallFilter(InvokerFilterChain.java:165)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:96)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDirectCallFilter(InvokerFilterChain.java:165)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:96)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDirectCallFilter(InvokerFilterChain.java:185)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:96)
    at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilter.doFilter(InvokerFilter.java:119)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
    at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:748)
Caused by: javax.xml.bind.JAXBException: "model.notes" doesnt contain ObjectFactory.class or jaxb.index
    at com.sun.xml.internal.bind.v2.ContextFactory.createContext(ContextFactory.java:266)
    at sun.reflect.GeneratedMethodAccessor1140.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:171)
    at javax.xml.bind.ContextFinder.newInstance(ContextFinder.java:131)
    ... 195 more
chahuistle commented 6 years ago

Plot twist: works in production (old qnavigator) but our current development version produces the described error.

chahuistle commented 6 years ago

Fixed with 47bd9eb17498f111a29809bccb601e20d2642acc