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Posted to dev@stanbol.apache.org by Rajan Shah <ra...@gmail.com> on 2015/05/22 15:23:53 UTC
Ontology upload/delete issue
Hi,
I have observed following issue with ontology upload.
a. Upload becomes successful, however access is not possible
b. Delete doesn't seem to work
c. Exception is being thrown while uploading a new ontology
I would appreciate, if someone can help out pertaining to these issues.
Please find included detailed description at the end.
Thanks in advance,
Rajan
*Steps to re-crate:*
1. Create new scope "newsEvents" from the Scope Manager
2. Upload the ontology via curl command as follows:
curl -X POST -F file=@newsEvents.owl -F format=application/rdf+xml
http://localhost:9090/ontonet/ontology/newsEvents -u "admin"
3. The uploaded ontology shows up
[image: Inline image 2]
4. However, when trying to access the ontology it produces following error.
[image: Inline image 1]
Similarly for the following ontology
[image: Inline image 3]
Problem accessing /ontonet/
http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/:::http://www.omg.org/spec/FIGI/20140201/GlobalInstrumentIdentifiers/.
Reason:
Not Found
*Couple questions:*
1. If it's not a valid ontology, why it is not complaining in the first
place
2. If machine is connected to the internet and the file is accessible via
browsing through URL
http://www.aifb.uni-karlsruhe.de/WBS/uhe/ontologies/newsEvents.owl, why 404
occurs.
3. The delete doesn't seem to work. i.e. I can delete now newsEvents from
Scope Manager however it leaves the effect and doesn't delete the
newsEvents link
4. In some uploads, it throws following exception
The failing instruction (print stack trace for 2 more):
==> #list it.manageableOntologies as mana... [in template
"html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
at line 40, column 9]
at
org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:96)
at
org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
at
org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1154)
at
org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:571)
at
org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:378)
at
org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:368)
at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:262)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
at
org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:320)
at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:236)
at
org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373)
at
org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
at
org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
at
org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:219)
at
org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:336)
at
org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:297)
at
org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:93)
at
org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:50)
at
org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
at
org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:84)
at
org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
at
org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
at
org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
at
org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:208)
at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:271)
at
org.apache.stanbol.commons.cors.StanbolCorsFilter.doFilter(StanbolCorsFilter.java:68)
at
org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
at
org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
at
org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
at
org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
at
org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:84)
at
org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
at
org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
at
org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilterHttp(ResourceServingFilter.java:148)
at
org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilter(ResourceServingFilter.java:91)
at
org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
at
org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
at
org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
at
org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
at
org.apache.stanbol.commons.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:208)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAsPrivileged(Subject.java:536)
at
org.apache.stanbol.commons.security.auth.AuthenticatingFilter.doFilter(AuthenticatingFilter.java:177)
at
org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
at
org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
at
org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
at
org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
at
org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:76)
at
org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:49)
at
org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808)
at
org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:587)
at
org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221)
at
org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
at
org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
at
org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061)
at
org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at
org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
at
org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
at org.eclipse.jetty.server.Server.handle(Server.java:497)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
at
org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
at
org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
at
org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635)
at
org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException:
freemarker.template.TemplateModelException: get(manageableOntologies)
failed on instance of
org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See cause
exception.
The failing instruction (print stack trace for 2 more):
==> #list it.manageableOntologies as mana... [in template
"html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
at line 40, column 9]
at
org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:110)
at
org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:78)
at
org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:45)
at
org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:263)
at
org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250)
at
org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
at
org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:103)
at
org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
at
org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:88)
... 73 more
Caused by: freemarker.template.TemplateModelException:
get(manageableOntologies) failed on instance of
org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See cause
exception.
The failing instruction (print stack trace for 2 more):
==> #list it.manageableOntologies as mana... [in template
"html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
at line 40, column 9]
at freemarker.ext.beans.BeanModel.get(BeanModel.java:222)
at freemarker.core.Dot._eval(Dot.java:76)
at freemarker.core.Expression.eval(Expression.java:111)
at freemarker.core.IteratorBlock.accept(IteratorBlock.java:94)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.MixedContent.accept(MixedContent.java:93)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.Environment.visit(Environment.java:487)
at freemarker.core.BodyInstruction.accept(BodyInstruction.java:93)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.MixedContent.accept(MixedContent.java:93)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.Macro$Context.runMacro(Macro.java:209)
at freemarker.core.Environment.visit(Environment.java:694)
at freemarker.core.UnifiedCall.accept(UnifiedCall.java:116)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.EscapeBlock.accept(EscapeBlock.java:85)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.MixedContent.accept(MixedContent.java:93)
at freemarker.core.Environment.visit(Environment.java:265)
at freemarker.core.Environment.process(Environment.java:243)
at freemarker.template.Template.process(Template.java:277)
at
org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:103)
... 81 more
Caused by: java.lang.reflect.InvocationTargetException
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:606)
at freemarker.ext.beans.BeansWrapper.invokeMethod(BeansWrapper.java:912)
at
freemarker.ext.beans.BeanModel.invokeThroughDescriptor(BeanModel.java:275)
at freemarker.ext.beans.BeanModel.get(BeanModel.java:182)
... 103 more
Caused by: java.security.AccessControlException: access denied
("org.apache.clerezza.rdf.core.access.security.TcPermission"
"urn:x-localinstance:/ontologymanager.graph" "read")
at
java.security.AccessControlContext.checkPermission(AccessControlContext.java:372)
at java.security.AccessController.checkPermission(AccessController.java:559)
at
org.apache.clerezza.rdf.core.access.security.TcAccessController.checkReadPermission(TcAccessController.java:107)
at
org.apache.clerezza.rdf.core.access.TcManager.getTriples(TcManager.java:208)
at
org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.getMetaGraph(ClerezzaOntologyProvider.java:676)
at
org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.buildResource(ClerezzaOntologyProvider.java:218)
at
org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.getMapping(ClerezzaOntologyProvider.java:277)
at
org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:1067)
at
org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:129)
at
org.apache.stanbol.ontologymanager.web.resources.ScopeResource.getManageableOntologies(ScopeResource.java:342)
... 110 more
Re: Ontology upload/delete issue
Posted by Rajan Shah <ra...@gmail.com>.
Hi Rupert,
I believe, they seem to have changed path to RDF file as follows:
*http://www.omg.org/spec/FIGI/20140201/GlobalInstrumentIdentifiers-odm.xmi
<http://www.omg.org/spec/FIGI/20140201/GlobalInstrumentIdentifiers-odm.xmi>*
I am not sure, whether do I need to manually change the path in RDF file
itself
<!DOCTYPE rdf:RDF [
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY dct "http://purl.org/dc/terms/" >
<!ENTITY skos "http://www.w3.org/2004/02/skos/core#" >
<!ENTITY sm "http://www.omg.org/techprocess/ab/SpecificationMetadata/" >
<!ENTITY figi-gii "
http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/" >
]>
<rdf:RDF xmlns="http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/"
xml:base="http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
Thanks,
Rajan
On Fri, May 22, 2015 at 10:04 AM, Rajan Shah <ra...@gmail.com> wrote:
> Hi Rupert,
>
> Thanks again!
>
> These exceptions are gone, however it still doesn't work.
>
> *1. ScopeManager*
> Scope: GlobalInstrumentIdentifiers [exists]
>
> *2. Request to upload the file*
>
> curl -X POST -F file=@GlobalInstrumentIdentifiers.rdf -F
> format=application/rdf+xml
> http://localhost:9090/ontonet/ontology/GlobalInstrumentIdentifiers
>
> *3. It generates following response.*
>
> <title>Error 400 </title>
> </head>
> <body>
> <h2>HTTP ERROR: 400</h2>
> <p>Problem accessing /ontonet/ontology/GlobalInstrumentIdentifiers. Reason:
> <pre> Bad Request</pre></p>
> <hr /><i><small>Powered by Jetty://</small></i>
> </body>
> </html>
>
> Again, the file can be loaded within webprotege without any issue. I am
> not sure, whether I am missing anything here. I have attached the file for
> your reference and can also be accessed via
> http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/.
>
> With best regards,
> Rajan
>
> On Fri, May 22, 2015 at 9:35 AM, Rupert Westenthaler <
> rupert.westenthaler@gmail.com> wrote:
>
>> Hi Rajan,
>>
>> Looks like if the root cause is a Security Exception. Can you try to
>> launch Stanbol with the '-no-security' option.
>>
>> BTW: Images do get removed when sending mails to the list. So if you
>> want to share screenshot you need to put them on the Web and link to
>> them in the mail.
>>
>> best
>> Rupert
>>
>>
>> On Fri, May 22, 2015 at 3:23 PM, Rajan Shah <ra...@gmail.com> wrote:
>> > Hi,
>> >
>> > I have observed following issue with ontology upload.
>> >
>> > a. Upload becomes successful, however access is not possible
>> > b. Delete doesn't seem to work
>> > c. Exception is being thrown while uploading a new ontology
>> >
>> > I would appreciate, if someone can help out pertaining to these issues.
>> > Please find included detailed description at the end.
>> >
>> > Thanks in advance,
>> > Rajan
>> >
>> > Steps to re-crate:
>> >
>> > 1. Create new scope "newsEvents" from the Scope Manager
>> > 2. Upload the ontology via curl command as follows:
>> >
>> > curl -X POST -F file=@newsEvents.owl -F format=application/rdf+xml
>> > http://localhost:9090/ontonet/ontology/newsEvents -u "admin"
>> >
>> > 3. The uploaded ontology shows up
>> >
>> >
>> >
>> > 4. However, when trying to access the ontology it produces following
>> error.
>> >
>> >
>> >
>> > Similarly for the following ontology
>> >
>> >
>> >
>> >
>> > Problem accessing
>> > /ontonet/
>> http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/:::http://www.omg.org/spec/FIGI/20140201/GlobalInstrumentIdentifiers/
>> .
>> > Reason:
>> >
>> > Not Found
>> >
>> >
>> > Couple questions:
>> >
>> > 1. If it's not a valid ontology, why it is not complaining in the first
>> > place
>> >
>> > 2. If machine is connected to the internet and the file is accessible
>> via
>> > browsing through URL
>> > http://www.aifb.uni-karlsruhe.de/WBS/uhe/ontologies/newsEvents.owl,
>> why 404
>> > occurs.
>> >
>> > 3. The delete doesn't seem to work. i.e. I can delete now newsEvents
>> from
>> > Scope Manager however it leaves the effect and doesn't delete the
>> newsEvents
>> > link
>> >
>> > 4. In some uploads, it throws following exception
>> >
>> > The failing instruction (print stack trace for 2 more):
>> > ==> #list it.manageableOntologies as mana... [in template
>> >
>> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
>> > at line 40, column 9]
>> > at
>> >
>> org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:96)
>> > at
>> >
>> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
>> > at
>> >
>> org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1154)
>> > at
>> >
>> org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:571)
>> > at
>> >
>> org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:378)
>> > at
>> >
>> org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:368)
>> > at
>> org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:262)
>> > at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
>> > at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
>> > at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
>> > at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
>> > at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
>> > at
>> >
>> org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:320)
>> > at
>> org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:236)
>> > at
>> >
>> org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
>> > at
>> org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373)
>> > at
>> >
>> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
>> > at
>> >
>> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
>> > at
>> >
>> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:219)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:336)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:297)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:93)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:50)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
>> > at
>> >
>> org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:84)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
>> > at
>> com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:208)
>> > at
>> com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:271)
>> > at
>> >
>> org.apache.stanbol.commons.cors.StanbolCorsFilter.doFilter(StanbolCorsFilter.java:68)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:84)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
>> > at
>> >
>> org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilterHttp(ResourceServingFilter.java:148)
>> > at
>> >
>> org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilter(ResourceServingFilter.java:91)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
>> > at
>> >
>> org.apache.stanbol.commons.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:208)
>> > at java.security.AccessController.doPrivileged(Native Method)
>> > at javax.security.auth.Subject.doAsPrivileged(Subject.java:536)
>> > at
>> >
>> org.apache.stanbol.commons.security.auth.AuthenticatingFilter.doFilter(AuthenticatingFilter.java:177)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
>> > at
>> >
>> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:76)
>> > at
>> >
>> org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:49)
>> > at
>> >
>> org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67)
>> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
>> > at
>> org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808)
>> > at
>> >
>> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:587)
>> > at
>> >
>> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221)
>> > at
>> >
>> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127)
>> > at
>> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
>> > at
>> >
>> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
>> > at
>> >
>> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061)
>> > at
>> >
>> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
>> > at
>> >
>> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
>> > at
>> >
>> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
>> > at org.eclipse.jetty.server.Server.handle(Server.java:497)
>> > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
>> > at
>> >
>> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
>> > at
>> >
>> org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
>> > at
>> >
>> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635)
>> > at
>> >
>> org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555)
>> > at java.lang.Thread.run(Thread.java:745)
>> > Caused by: java.lang.RuntimeException:
>> > freemarker.template.TemplateModelException: get(manageableOntologies)
>> failed
>> > on instance of
>> > org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See
>> cause
>> > exception.
>> >
>> > The failing instruction (print stack trace for 2 more):
>> > ==> #list it.manageableOntologies as mana... [in template
>> >
>> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
>> > at line 40, column 9]
>> > at
>> >
>> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:110)
>> > at
>> >
>> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:78)
>> > at
>> >
>> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:45)
>> > at
>> >
>> org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:263)
>> > at
>> >
>> org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250)
>> > at
>> >
>> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
>> > at
>> >
>> org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:103)
>> > at
>> >
>> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
>> > at
>> >
>> org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:88)
>> > ... 73 more
>> > Caused by: freemarker.template.TemplateModelException:
>> > get(manageableOntologies) failed on instance of
>> > org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See
>> cause
>> > exception.
>> >
>> > The failing instruction (print stack trace for 2 more):
>> > ==> #list it.manageableOntologies as mana... [in template
>> >
>> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
>> > at line 40, column 9]
>> > at freemarker.ext.beans.BeanModel.get(BeanModel.java:222)
>> > at freemarker.core.Dot._eval(Dot.java:76)
>> > at freemarker.core.Expression.eval(Expression.java:111)
>> > at freemarker.core.IteratorBlock.accept(IteratorBlock.java:94)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.MixedContent.accept(MixedContent.java:93)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.Environment.visit(Environment.java:487)
>> > at freemarker.core.BodyInstruction.accept(BodyInstruction.java:93)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.MixedContent.accept(MixedContent.java:93)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.Macro$Context.runMacro(Macro.java:209)
>> > at freemarker.core.Environment.visit(Environment.java:694)
>> > at freemarker.core.UnifiedCall.accept(UnifiedCall.java:116)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.EscapeBlock.accept(EscapeBlock.java:85)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.MixedContent.accept(MixedContent.java:93)
>> > at freemarker.core.Environment.visit(Environment.java:265)
>> > at freemarker.core.Environment.process(Environment.java:243)
>> > at freemarker.template.Template.process(Template.java:277)
>> > at
>> >
>> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:103)
>> > ... 81 more
>> > Caused by: java.lang.reflect.InvocationTargetException
>> > 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:606)
>> > at freemarker.ext.beans.BeansWrapper.invokeMethod(BeansWrapper.java:912)
>> > at
>> >
>> freemarker.ext.beans.BeanModel.invokeThroughDescriptor(BeanModel.java:275)
>> > at freemarker.ext.beans.BeanModel.get(BeanModel.java:182)
>> > ... 103 more
>> > Caused by: java.security.AccessControlException: access denied
>> > ("org.apache.clerezza.rdf.core.access.security.TcPermission"
>> > "urn:x-localinstance:/ontologymanager.graph" "read")
>> > at
>> >
>> java.security.AccessControlContext.checkPermission(AccessControlContext.java:372)
>> > at
>> java.security.AccessController.checkPermission(AccessController.java:559)
>> > at
>> >
>> org.apache.clerezza.rdf.core.access.security.TcAccessController.checkReadPermission(TcAccessController.java:107)
>> > at
>> >
>> org.apache.clerezza.rdf.core.access.TcManager.getTriples(TcManager.java:208)
>> > at
>> >
>> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.getMetaGraph(ClerezzaOntologyProvider.java:676)
>> > at
>> >
>> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.buildResource(ClerezzaOntologyProvider.java:218)
>> > at
>> >
>> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.getMapping(ClerezzaOntologyProvider.java:277)
>> > at
>> >
>> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:1067)
>> > at
>> >
>> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:129)
>> > at
>> >
>> org.apache.stanbol.ontologymanager.web.resources.ScopeResource.getManageableOntologies(ScopeResource.java:342)
>> > ... 110 more
>> >
>> >
>> >
>>
>>
>>
>> --
>> | Rupert Westenthaler rupert.westenthaler@gmail.com
>> | Bodenlehenstraße 11 ++43-699-11108907
>> | A-5500 Bischofshofen
>> | REDLINK.CO
>> ..........................................................................
>> | http://redlink.co/
>>
>
>
Re: Ontology upload/delete issue
Posted by Rajan Shah <ra...@gmail.com>.
Hi Rupert,
Thanks again!
These exceptions are gone, however it still doesn't work.
*1. ScopeManager*
Scope: GlobalInstrumentIdentifiers [exists]
*2. Request to upload the file*
curl -X POST -F file=@GlobalInstrumentIdentifiers.rdf -F
format=application/rdf+xml
http://localhost:9090/ontonet/ontology/GlobalInstrumentIdentifiers
*3. It generates following response.*
<title>Error 400 </title>
</head>
<body>
<h2>HTTP ERROR: 400</h2>
<p>Problem accessing /ontonet/ontology/GlobalInstrumentIdentifiers. Reason:
<pre> Bad Request</pre></p>
<hr /><i><small>Powered by Jetty://</small></i>
</body>
</html>
Again, the file can be loaded within webprotege without any issue. I am not
sure, whether I am missing anything here. I have attached the file for your
reference and can also be accessed via
http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/.
With best regards,
Rajan
On Fri, May 22, 2015 at 9:35 AM, Rupert Westenthaler <
rupert.westenthaler@gmail.com> wrote:
> Hi Rajan,
>
> Looks like if the root cause is a Security Exception. Can you try to
> launch Stanbol with the '-no-security' option.
>
> BTW: Images do get removed when sending mails to the list. So if you
> want to share screenshot you need to put them on the Web and link to
> them in the mail.
>
> best
> Rupert
>
>
> On Fri, May 22, 2015 at 3:23 PM, Rajan Shah <ra...@gmail.com> wrote:
> > Hi,
> >
> > I have observed following issue with ontology upload.
> >
> > a. Upload becomes successful, however access is not possible
> > b. Delete doesn't seem to work
> > c. Exception is being thrown while uploading a new ontology
> >
> > I would appreciate, if someone can help out pertaining to these issues.
> > Please find included detailed description at the end.
> >
> > Thanks in advance,
> > Rajan
> >
> > Steps to re-crate:
> >
> > 1. Create new scope "newsEvents" from the Scope Manager
> > 2. Upload the ontology via curl command as follows:
> >
> > curl -X POST -F file=@newsEvents.owl -F format=application/rdf+xml
> > http://localhost:9090/ontonet/ontology/newsEvents -u "admin"
> >
> > 3. The uploaded ontology shows up
> >
> >
> >
> > 4. However, when trying to access the ontology it produces following
> error.
> >
> >
> >
> > Similarly for the following ontology
> >
> >
> >
> >
> > Problem accessing
> > /ontonet/
> http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/:::http://www.omg.org/spec/FIGI/20140201/GlobalInstrumentIdentifiers/
> .
> > Reason:
> >
> > Not Found
> >
> >
> > Couple questions:
> >
> > 1. If it's not a valid ontology, why it is not complaining in the first
> > place
> >
> > 2. If machine is connected to the internet and the file is accessible via
> > browsing through URL
> > http://www.aifb.uni-karlsruhe.de/WBS/uhe/ontologies/newsEvents.owl, why
> 404
> > occurs.
> >
> > 3. The delete doesn't seem to work. i.e. I can delete now newsEvents from
> > Scope Manager however it leaves the effect and doesn't delete the
> newsEvents
> > link
> >
> > 4. In some uploads, it throws following exception
> >
> > The failing instruction (print stack trace for 2 more):
> > ==> #list it.manageableOntologies as mana... [in template
> >
> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
> > at line 40, column 9]
> > at
> >
> org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:96)
> > at
> >
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
> > at
> >
> org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1154)
> > at
> >
> org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:571)
> > at
> >
> org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:378)
> > at
> >
> org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:368)
> > at
> org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:262)
> > at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
> > at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
> > at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
> > at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
> > at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
> > at
> >
> org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:320)
> > at
> org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:236)
> > at
> >
> org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
> > at
> org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373)
> > at
> >
> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
> > at
> >
> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
> > at
> >
> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:219)
> > at
> >
> org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:336)
> > at
> >
> org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:297)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:93)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:50)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> > at
> >
> org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:84)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> > at
> com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:208)
> > at
> com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:271)
> > at
> >
> org.apache.stanbol.commons.cors.StanbolCorsFilter.doFilter(StanbolCorsFilter.java:68)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:84)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> > at
> >
> org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilterHttp(ResourceServingFilter.java:148)
> > at
> >
> org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilter(ResourceServingFilter.java:91)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> > at
> >
> org.apache.stanbol.commons.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:208)
> > at java.security.AccessController.doPrivileged(Native Method)
> > at javax.security.auth.Subject.doAsPrivileged(Subject.java:536)
> > at
> >
> org.apache.stanbol.commons.security.auth.AuthenticatingFilter.doFilter(AuthenticatingFilter.java:177)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> > at
> >
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:76)
> > at
> >
> org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:49)
> > at
> >
> org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
> > at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808)
> > at
> >
> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:587)
> > at
> >
> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221)
> > at
> >
> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127)
> > at
> org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
> > at
> >
> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
> > at
> >
> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061)
> > at
> >
> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
> > at
> >
> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
> > at
> >
> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
> > at org.eclipse.jetty.server.Server.handle(Server.java:497)
> > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
> > at
> >
> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
> > at
> >
> org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
> > at
> >
> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635)
> > at
> >
> org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555)
> > at java.lang.Thread.run(Thread.java:745)
> > Caused by: java.lang.RuntimeException:
> > freemarker.template.TemplateModelException: get(manageableOntologies)
> failed
> > on instance of
> > org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See cause
> > exception.
> >
> > The failing instruction (print stack trace for 2 more):
> > ==> #list it.manageableOntologies as mana... [in template
> >
> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
> > at line 40, column 9]
> > at
> >
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:110)
> > at
> >
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:78)
> > at
> >
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:45)
> > at
> >
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:263)
> > at
> >
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250)
> > at
> >
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
> > at
> >
> org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:103)
> > at
> >
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
> > at
> >
> org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:88)
> > ... 73 more
> > Caused by: freemarker.template.TemplateModelException:
> > get(manageableOntologies) failed on instance of
> > org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See cause
> > exception.
> >
> > The failing instruction (print stack trace for 2 more):
> > ==> #list it.manageableOntologies as mana... [in template
> >
> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
> > at line 40, column 9]
> > at freemarker.ext.beans.BeanModel.get(BeanModel.java:222)
> > at freemarker.core.Dot._eval(Dot.java:76)
> > at freemarker.core.Expression.eval(Expression.java:111)
> > at freemarker.core.IteratorBlock.accept(IteratorBlock.java:94)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.MixedContent.accept(MixedContent.java:93)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.Environment.visit(Environment.java:487)
> > at freemarker.core.BodyInstruction.accept(BodyInstruction.java:93)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.MixedContent.accept(MixedContent.java:93)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.Macro$Context.runMacro(Macro.java:209)
> > at freemarker.core.Environment.visit(Environment.java:694)
> > at freemarker.core.UnifiedCall.accept(UnifiedCall.java:116)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.EscapeBlock.accept(EscapeBlock.java:85)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.MixedContent.accept(MixedContent.java:93)
> > at freemarker.core.Environment.visit(Environment.java:265)
> > at freemarker.core.Environment.process(Environment.java:243)
> > at freemarker.template.Template.process(Template.java:277)
> > at
> >
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:103)
> > ... 81 more
> > Caused by: java.lang.reflect.InvocationTargetException
> > 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:606)
> > at freemarker.ext.beans.BeansWrapper.invokeMethod(BeansWrapper.java:912)
> > at
> >
> freemarker.ext.beans.BeanModel.invokeThroughDescriptor(BeanModel.java:275)
> > at freemarker.ext.beans.BeanModel.get(BeanModel.java:182)
> > ... 103 more
> > Caused by: java.security.AccessControlException: access denied
> > ("org.apache.clerezza.rdf.core.access.security.TcPermission"
> > "urn:x-localinstance:/ontologymanager.graph" "read")
> > at
> >
> java.security.AccessControlContext.checkPermission(AccessControlContext.java:372)
> > at
> java.security.AccessController.checkPermission(AccessController.java:559)
> > at
> >
> org.apache.clerezza.rdf.core.access.security.TcAccessController.checkReadPermission(TcAccessController.java:107)
> > at
> >
> org.apache.clerezza.rdf.core.access.TcManager.getTriples(TcManager.java:208)
> > at
> >
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.getMetaGraph(ClerezzaOntologyProvider.java:676)
> > at
> >
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.buildResource(ClerezzaOntologyProvider.java:218)
> > at
> >
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.getMapping(ClerezzaOntologyProvider.java:277)
> > at
> >
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:1067)
> > at
> >
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:129)
> > at
> >
> org.apache.stanbol.ontologymanager.web.resources.ScopeResource.getManageableOntologies(ScopeResource.java:342)
> > ... 110 more
> >
> >
> >
>
>
>
> --
> | Rupert Westenthaler rupert.westenthaler@gmail.com
> | Bodenlehenstraße 11 ++43-699-11108907
> | A-5500 Bischofshofen
> | REDLINK.CO
> ..........................................................................
> | http://redlink.co/
>
Re: Ontology upload/delete issue
Posted by Rupert Westenthaler <ru...@gmail.com>.
Hi Rajan,
Looks like if the root cause is a Security Exception. Can you try to
launch Stanbol with the '-no-security' option.
BTW: Images do get removed when sending mails to the list. So if you
want to share screenshot you need to put them on the Web and link to
them in the mail.
best
Rupert
On Fri, May 22, 2015 at 3:23 PM, Rajan Shah <ra...@gmail.com> wrote:
> Hi,
>
> I have observed following issue with ontology upload.
>
> a. Upload becomes successful, however access is not possible
> b. Delete doesn't seem to work
> c. Exception is being thrown while uploading a new ontology
>
> I would appreciate, if someone can help out pertaining to these issues.
> Please find included detailed description at the end.
>
> Thanks in advance,
> Rajan
>
> Steps to re-crate:
>
> 1. Create new scope "newsEvents" from the Scope Manager
> 2. Upload the ontology via curl command as follows:
>
> curl -X POST -F file=@newsEvents.owl -F format=application/rdf+xml
> http://localhost:9090/ontonet/ontology/newsEvents -u "admin"
>
> 3. The uploaded ontology shows up
>
>
>
> 4. However, when trying to access the ontology it produces following error.
>
>
>
> Similarly for the following ontology
>
>
>
>
> Problem accessing
> /ontonet/http://www.omg.org/spec/FIGI/GlobalInstrumentIdentifiers/:::http://www.omg.org/spec/FIGI/20140201/GlobalInstrumentIdentifiers/.
> Reason:
>
> Not Found
>
>
> Couple questions:
>
> 1. If it's not a valid ontology, why it is not complaining in the first
> place
>
> 2. If machine is connected to the internet and the file is accessible via
> browsing through URL
> http://www.aifb.uni-karlsruhe.de/WBS/uhe/ontologies/newsEvents.owl, why 404
> occurs.
>
> 3. The delete doesn't seem to work. i.e. I can delete now newsEvents from
> Scope Manager however it leaves the effect and doesn't delete the newsEvents
> link
>
> 4. In some uploads, it throws following exception
>
> The failing instruction (print stack trace for 2 more):
> ==> #list it.manageableOntologies as mana... [in template
> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
> at line 40, column 9]
> at
> org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:96)
> at
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
> at
> org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1154)
> at
> org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:571)
> at
> org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:378)
> at
> org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:368)
> at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:262)
> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
> at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
> at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
> at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
> at
> org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:320)
> at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:236)
> at
> org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
> at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:373)
> at
> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
> at
> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
> at
> org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:219)
> at
> org.apache.felix.http.base.internal.handler.ServletHandler.doHandle(ServletHandler.java:336)
> at
> org.apache.felix.http.base.internal.handler.ServletHandler.handle(ServletHandler.java:297)
> at
> org.apache.felix.http.base.internal.dispatch.ServletPipeline.handle(ServletPipeline.java:93)
> at
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:50)
> at
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> at
> org.apache.stanbol.commons.httpqueryheaders.impl.QueryHeadersFilter.doFilter(QueryHeadersFilter.java:84)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> at
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> at
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:208)
> at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:271)
> at
> org.apache.stanbol.commons.cors.StanbolCorsFilter.doFilter(StanbolCorsFilter.java:68)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> at
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> at
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:84)
> at
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> at
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> at
> org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilterHttp(ResourceServingFilter.java:148)
> at
> org.apache.stanbol.commons.web.resources.ResourceServingFilter.doFilter(ResourceServingFilter.java:91)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> at
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> at
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> at
> org.apache.stanbol.commons.security.auth.AuthenticatingFilter$1.run(AuthenticatingFilter.java:208)
> at java.security.AccessController.doPrivileged(Native Method)
> at javax.security.auth.Subject.doAsPrivileged(Subject.java:536)
> at
> org.apache.stanbol.commons.security.auth.AuthenticatingFilter.doFilter(AuthenticatingFilter.java:177)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.doHandle(FilterHandler.java:108)
> at
> org.apache.felix.http.base.internal.handler.FilterHandler.handle(FilterHandler.java:80)
> at
> org.apache.felix.http.base.internal.dispatch.InvocationFilterChain.doFilter(InvocationFilterChain.java:46)
> at
> org.apache.felix.http.base.internal.dispatch.HttpFilterChain.doFilter(HttpFilterChain.java:31)
> at
> org.apache.felix.http.base.internal.dispatch.FilterPipeline.dispatch(FilterPipeline.java:76)
> at
> org.apache.felix.http.base.internal.dispatch.Dispatcher.dispatch(Dispatcher.java:49)
> at
> org.apache.felix.http.base.internal.DispatcherServlet.service(DispatcherServlet.java:67)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
> at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808)
> at
> org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:587)
> at
> org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221)
> at
> org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127)
> at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
> at
> org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
> at
> org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061)
> at
> org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
> at
> org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
> at
> org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
> at org.eclipse.jetty.server.Server.handle(Server.java:497)
> at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
> at
> org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257)
> at
> org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
> at
> org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635)
> at
> org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.lang.RuntimeException:
> freemarker.template.TemplateModelException: get(manageableOntologies) failed
> on instance of
> org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See cause
> exception.
>
> The failing instruction (print stack trace for 2 more):
> ==> #list it.manageableOntologies as mana... [in template
> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
> at line 40, column 9]
> at
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:110)
> at
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:78)
> at
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.writeTo(ViewableWriter.java:45)
> at
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:263)
> at
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250)
> at
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
> at
> org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:103)
> at
> org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
> at
> org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:88)
> ... 73 more
> Caused by: freemarker.template.TemplateModelException:
> get(manageableOntologies) failed on instance of
> org.apache.stanbol.ontologymanager.web.resources.ScopeResource. See cause
> exception.
>
> The failing instruction (print stack trace for 2 more):
> ==> #list it.manageableOntologies as mana... [in template
> "html/org/apache/stanbol/ontologymanager/web/resources/ScopeResource/index"
> at line 40, column 9]
> at freemarker.ext.beans.BeanModel.get(BeanModel.java:222)
> at freemarker.core.Dot._eval(Dot.java:76)
> at freemarker.core.Expression.eval(Expression.java:111)
> at freemarker.core.IteratorBlock.accept(IteratorBlock.java:94)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.MixedContent.accept(MixedContent.java:93)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.Environment.visit(Environment.java:487)
> at freemarker.core.BodyInstruction.accept(BodyInstruction.java:93)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.MixedContent.accept(MixedContent.java:93)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.Macro$Context.runMacro(Macro.java:209)
> at freemarker.core.Environment.visit(Environment.java:694)
> at freemarker.core.UnifiedCall.accept(UnifiedCall.java:116)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.EscapeBlock.accept(EscapeBlock.java:85)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.MixedContent.accept(MixedContent.java:93)
> at freemarker.core.Environment.visit(Environment.java:265)
> at freemarker.core.Environment.process(Environment.java:243)
> at freemarker.template.Template.process(Template.java:277)
> at
> org.apache.stanbol.commons.viewable.writer.impl.ViewableWriter.renderPojo(ViewableWriter.java:103)
> ... 81 more
> Caused by: java.lang.reflect.InvocationTargetException
> 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:606)
> at freemarker.ext.beans.BeansWrapper.invokeMethod(BeansWrapper.java:912)
> at
> freemarker.ext.beans.BeanModel.invokeThroughDescriptor(BeanModel.java:275)
> at freemarker.ext.beans.BeanModel.get(BeanModel.java:182)
> ... 103 more
> Caused by: java.security.AccessControlException: access denied
> ("org.apache.clerezza.rdf.core.access.security.TcPermission"
> "urn:x-localinstance:/ontologymanager.graph" "read")
> at
> java.security.AccessControlContext.checkPermission(AccessControlContext.java:372)
> at java.security.AccessController.checkPermission(AccessController.java:559)
> at
> org.apache.clerezza.rdf.core.access.security.TcAccessController.checkReadPermission(TcAccessController.java:107)
> at
> org.apache.clerezza.rdf.core.access.TcManager.getTriples(TcManager.java:208)
> at
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.getMetaGraph(ClerezzaOntologyProvider.java:676)
> at
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.buildResource(ClerezzaOntologyProvider.java:218)
> at
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider$OntologyToTcMapper.getMapping(ClerezzaOntologyProvider.java:277)
> at
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:1067)
> at
> org.apache.stanbol.ontologymanager.multiplexer.clerezza.ontology.ClerezzaOntologyProvider.listPrimaryKeys(ClerezzaOntologyProvider.java:129)
> at
> org.apache.stanbol.ontologymanager.web.resources.ScopeResource.getManageableOntologies(ScopeResource.java:342)
> ... 110 more
>
>
>
--
| Rupert Westenthaler rupert.westenthaler@gmail.com
| Bodenlehenstraße 11 ++43-699-11108907
| A-5500 Bischofshofen
| REDLINK.CO ..........................................................................
| http://redlink.co/