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[bioontology-support] Bioportal AMI virtual appliance: Error parsing ontology

Paul R Alexander palexander at stanford.edu
Wed Dec 19 15:44:51 PST 2012


Xavier,

We've actually had trouble parsing this ontology ourselves. I believe in this instance we had to use a local copy of Protege to parse and dump the ontology to a database table, which we then used in BioPortal. I can supply that table to you and you could do some manual updates to get the ontology working in your AMI instance if that would work for you.

Paul


On Dec 18, 2012, at 4:23 PM, "Schildwachter, Xavier" <x.schildwachter at sagebase.org> wrote:

> Hello,
> I downloaded http://bioportal.bioontology.org/ontologies/3022 and uploaded it
> in my Bioportal instance. In Admin portal, selected ‘Parse Ontologies’, input id,
> choose default parser nd clicked Run.
> Came back a while later to find the message below.
>  
> Thanks - Xavier
>  
> The following error has occurred:
> org.ncbo.stanford.admin.view.bean.response.HttpResponseSuccessBean cannot be cast to org.ncbo.stanford.admin.view.bean.response.HttpResponseErrorBean
>  
> Please copy the information below and mail it to the BioPortal development team:
>  
> java.lang.ClassCastException: org.ncbo.stanford.admin.view.bean.response.HttpResponseSuccessBean cannot be cast to org.ncbo.stanford.admin.view.bean.response.HttpResponseErrorBean
> at org.ncbo.stanford.admin.view.rest.RESTManager.populateErrorBean(RESTManager.java:493)
> at org.ncbo.stanford.admin.view.rest.RESTManager.processPost(RESTManager.java:398)
> at org.ncbo.stanford.admin.view.rest.RESTManager.parseOntologies(RESTManager.java:198)
> at org.ncbo.stanford.admin.view.bean.ontology.ParseOntologiesManagerBean.parseOntologies(ParseOntologiesManagerBean.java:17)
> 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:616)
> at org.apache.el.parser.AstValue.invoke(AstValue.java:191)
> at org.apache.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:276)
> at com.sun.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:68)
> at javax.faces.component._MethodExpressionToMethodBinding.invoke(_MethodExpressionToMethodBinding.java:88)
> at org.apache.myfaces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:100)
> at javax.faces.component.UICommand.broadcast(UICommand.java:120)
> at javax.faces.component.UIViewRoot._broadcastAll(UIViewRoot.java:889)
> at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:238)
> at javax.faces.component.UIViewRoot._process(UIViewRoot.java:1201)
> at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:627
> at org.apache.myfaces.lifecycle.InvokeApplicationExecutor.execute(InvokeApplicationExecutor.java:34)
> at org.apache.myfaces.lifecycle.LifecycleImpl.executePhase(LifecycleImpl.java:171)
> at org.apache.myfaces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:118)
> at javax.faces.webapp.FacesServlet.service(FacesServlet.java:189)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
> at org.ncbo.stanford.admin.view.filter.AuthenticationCheckFilter.doFilter(AuthenticationCheckFilter.java:75)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
> at org.apache.myfaces.webapp.filter.ExtensionsFilter.doFilter(ExtensionsFilter.java:341)
> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
> 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.StandardEngineValve.invoke(StandardEngineValve.java:109)
> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
> at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:877)
> at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:594)
> at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1675) at java.lang.Thread.run(Thread.java:679)
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> bioontology-support at lists.stanford.edu
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