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[bioontology-support] Fwd: OntoPortal visualization module

John Graybeal jgraybeal at stanford.edu
Thu Apr 4 09:45:21 PDT 2019



From: "Madani, Sina"
Date: Tuesday, April 2, 2019 at 11:45 AM
Subject: Re: OntoPortal visualization module

Hi,

Is the content in this wiki page still valid for OntoPortal 2.5 and/or do we need to activate visualization module in our local version of OntoPortal? The “Menu” icon in visualization context that is mentioned in the page doesn’t seem to exist in the frame and “mapping neighborhood” always remain in the “connecting” mode without any result (for two very small local ontologies).

https://www.bioontology.org/wiki/Visualizing_Concepts_and_Mappings

Thanks!

Sina



[cid:image001.png at 01D4E949.9EA3DB10]

Apr 02, 2019 9:10:18 AM org.thechiselgroup.biomixer.client.core.util.task.LogErrorTaskExecutor execute
SEVERE: null
java.lang.NullPointerException
                at com.google.appengine.api.users.UserServiceImpl.isUserLoggedIn(UserServiceImpl.java:89)
                at org.thechiselgroup.biomixer.server.workbench.authentication.DefaultAuthenticationService.getAuthentication(DefaultAuthenticationService.java:39)
                at org.thechiselgroup.biomixer.server.workbench.authentication.AuthenticationServiceServlet$1.execute(AuthenticationServiceServlet.java:38)
                at org.thechiselgroup.biomixer.server.workbench.authentication.AuthenticationServiceServlet$1.execute(AuthenticationServiceServlet.java:1)
                at org.thechiselgroup.biomixer.client.core.util.task.DirectTaskExecutor.execute(DirectTaskExecutor.java:22)
                at org.thechiselgroup.biomixer.client.core.util.task.DelegatingTaskExecutor.execute(DelegatingTaskExecutor.java:29)
                at org.thechiselgroup.biomixer.client.core.util.task.LogErrorTaskExecutor.execute(LogErrorTaskExecutor.java:35)
                at org.thechiselgroup.biomixer.server.workbench.server.ChooselServiceServlet.execute(ChooselServiceServlet.java:37)
                at org.thechiselgroup.biomixer.server.workbench.authentication.AuthenticationServiceServlet.getAuthentication(AuthenticationServiceServlet.java:35)
                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.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:561)
                at com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:208)
                at com.google.gwt.user.server.rpc.RemoteServiceServlet.processPost(RemoteServiceServlet.java:248)
                at com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet.doPost(AbstractRemoteServiceServlet.java:62)
                at javax.servlet.http.HttpServlet.service(HttpServlet.java:643)
                at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
                at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
                at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
                at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
                at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
                at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
                at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
                at org.apache.catalina.core.StandardEngineVal


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