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[bioontology-support] OntoPortal visualization module

Madani, Sina Sina.Madani at vumc.org
Thu Apr 4 14:51:06 PDT 2019


Thank you very much Jennifer!

Another thing that I noticed today is that the visualizer only shows 3 types of arcs: part-of, is-a, and mapping. Not sure if this is by design but showing arcs from object properties included in an ontology would be great.

Sina

On Apr 4, 2019, at 4:45 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sina,

Yes, that wiki page is still valid. I looked at another installation of the virtual appliance, and the issues you reported below with the visualization software are present there as well. We’ve entered a couple of issues in our tracker so that we can look into it:

https://github.com/ncbo/virtual_appliance/issues/6<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fvirtual_appliance%2Fissues%2F6&data=02%7C01%7CSina.Madani%40vumc.org%7Cc0770b0cf61943d5130608d6b946d2f8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636900111171971741&sdata=QTYpIMdU9OIWhKXIThC1EDSur0BPrTFvWXJnOf2lFMw%3D&reserved=0>
https://github.com/ncbo/virtual_appliance/issues/7<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fvirtual_appliance%2Fissues%2F7&data=02%7C01%7CSina.Madani%40vumc.org%7Cc0770b0cf61943d5130608d6b946d2f8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636900111171981750&sdata=ouoZqRwpE8Plp9rdsmweEQkRJ3gYiTjZqdTFTD96OPM%3D&reserved=0>

Kind regards,
Jennifer



On Apr 4, 2019, at 9:45 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:



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<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bioontology.org%2Fwiki%2FVisualizing_Concepts_and_Mappings&data=02%7C01%7CSina.Madani%40vumc.org%7Cc0770b0cf61943d5130608d6b946d2f8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C636900111171981750&sdata=a6Tq1dLvkCZ6T8Eig2n%2B%2FRujbHX3qokA9YsEnX46Dyk%3D&reserved=0>

Thanks!

Sina



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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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