ERROR: Query evaluation exception caught

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Lam Nguyen

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May 1, 2022, 8:44:44 PM5/1/22
to vocbench-user
Dear Vocbench3 development team,
I am a newbie to using vocbench3 version 10.2.1.
I could install vocbench3 using docker.
I created a test project in OWL format.

I got this error when I click to access data and click to thing class. It displayed the error message on the console but the software is still running and working. I don't what is the error behind the screen.

ERROR [qtp1896147296-365] Query evaluation exception caught
org.eclipse.rdf4j.query.QueryEvaluationException: Unsupported value expr type: class org.eclipse.rdf4j.query.algebra.Min
    at org.eclipse.rdf4j.query.algebra.evaluation.impl.StrictEvaluationStrategy.evaluate(StrictEvaluationStrategy.java:1090)
    at org.eclipse.rdf4j.query.algebra.evaluation.impl.ConstantOptimizer$ConstantVisitor.meetUnaryValueOperator(ConstantOptimizer.java:198)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meet(AbstractQueryModelVisitor.java:355)
    at org.eclipse.rdf4j.query.algebra.Min.visit(Min.java:25)
    at org.eclipse.rdf4j.query.algebra.ExtensionElem.visitChildren(ExtensionElem.java:61)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetNode(AbstractQueryModelVisitor.java:572)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meet(AbstractQueryModelVisitor.java:225)
    at org.eclipse.rdf4j.query.algebra.ExtensionElem.visit(ExtensionElem.java:56)
    at org.eclipse.rdf4j.query.algebra.Extension.visitChildren(Extension.java:98)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetNode(AbstractQueryModelVisitor.java:572)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetUnaryTupleOperator(AbstractQueryModelVisitor.java:592)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meet(AbstractQueryModelVisitor.java:220)
    at org.eclipse.rdf4j.query.algebra.Extension.visit(Extension.java:91)
    at org.eclipse.rdf4j.query.algebra.UnaryTupleOperator.visitChildren(UnaryTupleOperator.java:79)
    at org.eclipse.rdf4j.query.algebra.Projection.visitChildren(Projection.java:81)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetNode(AbstractQueryModelVisitor.java:572)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetUnaryTupleOperator(AbstractQueryModelVisitor.java:592)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meet(AbstractQueryModelVisitor.java:400)
    at org.eclipse.rdf4j.query.algebra.Projection.visit(Projection.java:75)
    at org.eclipse.rdf4j.query.algebra.UnaryTupleOperator.visitChildren(UnaryTupleOperator.java:79)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetNode(AbstractQueryModelVisitor.java:572)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetUnaryTupleOperator(AbstractQueryModelVisitor.java:592)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meet(AbstractQueryModelVisitor.java:450)
    at org.eclipse.rdf4j.query.algebra.Slice.visit(Slice.java:85)
    at org.eclipse.rdf4j.query.algebra.UnaryTupleOperator.visitChildren(UnaryTupleOperator.java:79)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meetNode(AbstractQueryModelVisitor.java:572)
    at org.eclipse.rdf4j.query.algebra.helpers.AbstractQueryModelVisitor.meet(AbstractQueryModelVisitor.java:415)
    at org.eclipse.rdf4j.query.algebra.QueryRoot.visit(QueryRoot.java:45)
    at org.eclipse.rdf4j.query.algebra.evaluation.impl.ConstantOptimizer.optimize(ConstantOptimizer.java:72)
    at org.eclipse.rdf4j.query.algebra.evaluation.impl.StrictEvaluationStrategy.optimize(StrictEvaluationStrategy.java:272)
    at org.eclipse.rdf4j.sail.base.SailSourceConnection.evaluateInternal(SailSourceConnection.java:244)
    at org.eclipse.rdf4j.sail.helpers.AbstractSailConnection.evaluate(AbstractSailConnection.java:249)
    at org.eclipse.rdf4j.repository.sail.SailTupleQuery.evaluate(SailTupleQuery.java:50)
    at it.uniroma2.art.semanticturkey.mdr.core.impl.MetadataRegistryBackendImpl.listDatasetMetadata(MetadataRegistryBackendImpl.java:1195)
    at it.uniroma2.art.semanticturkey.mdr.core.impl.MetadataRegistryBackendImpl.getDatasetMetadata(MetadataRegistryBackendImpl.java:1201)
    at it.uniroma2.art.semanticturkey.mdr.core.impl.MetadataRegistryBackendImpl.findDatasetForResource(MetadataRegistryBackendImpl.java:1337)
    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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
    at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:58)
    at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:62)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:132)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:120)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:56)
    at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:39)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.osgi.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:59)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:132)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:120)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
    at com.sun.proxy.$Proxy111.findDatasetForResource(Unknown Source)
    at it.uniroma2.art.semanticturkey.data.access.ResourceLocator.locateResource(ResourceLocator.java:107)
    at it.uniroma2.art.semanticturkey.data.access.ResourceLocator.locateResource(ResourceLocator.java:129)
    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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
    at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:58)
    at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:62)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:132)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:120)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:56)
    at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:39)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.osgi.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:59)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:132)
    at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:120)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.CglibAopProxy$FixedChainStaticTargetInterceptor.intercept(CglibAopProxy.java:584)
    at it.uniroma2.art.semanticturkey.data.access.ResourceLocator$$EnhancerBySpringCGLIB$$796b4d52.locateResource(<generated>)
    at it.uniroma2.art.semanticturkey.services.core.Resources.getResourcesPosition(Resources.java:336)
    at it.uniroma2.art.semanticturkey.services.core.Resources$$FastClassBySpringCGLIB$$4d9acdf1.invoke(<generated>)
    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:701)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
    at org.springframework.validation.beanvalidation.MethodValidationInterceptor.invoke(MethodValidationInterceptor.java:93)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:64)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:96)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:260)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:51)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161)
    at org.springframework.aop.aspectj.AspectJAfterAdvice.invoke(AspectJAfterAdvice.java:42)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:161)
    at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:91)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:633)
    at it.uniroma2.art.semanticturkey.services.core.Resources$$EnhancerBySpringCGLIB$$b567e54f.getResourcesPosition(<generated>)
    at it.uniroma2.art.semanticturkey.services.core.controllers.ResourcesController.getResourcesPositionPublished(ResourcesController.java:114)
    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 org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221)
    at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136)
    at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:743)
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:672)
    at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:82)
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:933)
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:951)
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:853)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:707)
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:827)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
    at org.eclipse.jetty.servlet.ServletHolder$NotAsync.service(ServletHolder.java:1459)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:799)
    at org.eclipse.jetty.servlet.ServletHandler$ChainEnd.doFilter(ServletHandler.java:1626)
    at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:228)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:186)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:166)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:146)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:54)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.ui.DefaultLoginPageGeneratingFilter.doFilter(DefaultLoginPageGeneratingFilter.java:91)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:183)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:105)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:125)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at it.uniroma2.art.semanticturkey.security.CORSFilter.doFilter(CORSFilter.java:40)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.saml.metadata.MetadataGeneratorFilter.doFilter(MetadataGeneratorFilter.java:87)
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:343)
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:260)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:193)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
    at it.uniroma2.art.semanticturkey.http.session.CrossContextSessionFilter.doFilter(CrossContextSessionFilter.java:25)
    at org.eclipse.jetty.servlet.FilterHolder.doFilter(FilterHolder.java:201)
    at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1601)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:548)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:71)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:602)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:235)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1624)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:233)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1434)
    at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:298)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:188)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:501)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1594)
    at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:186)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1349)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
    at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:82)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127)
    at org.eclipse.jetty.server.Server.handle(Server.java:516)
    at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:388)
    at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:633)
    at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:380)
    at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277)
    at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311)
    at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105)
    at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask(EatWhatYouKill.java:338)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:315)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce(EatWhatYouKill.java:173)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
    at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:386)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034)
    at java.lang.Thread.run(Thread.java:750)

Tiziano Lorenzetti

unread,
May 2, 2022, 8:14:15 AM5/2/22
to Lam Nguyen, vocbench-user
Dear Lam,
unfortunately this is something that doesn't depend directly from VB but it is an issue with RDF4J 3.7.3 (https://github.com/eclipse/rdf4j/issues/3414) which has not yet been resolved.
The good news is that it doesn't affect the correct behaviour of VB.
However, we are looking for a way to prevent these annoying messages from constantly printing on the console.

Best regards,
Tiziano


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Lam Nguyen

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May 2, 2022, 8:49:38 AM5/2/22
to Tiziano Lorenzetti, vocbench-user
Dear Tinizano,

Thanks for your reply. 

Another question regarding connection database. Is it possible to connect VB ontology using python. I would like to update graph database using programing language and others can see on VB system intermediately. 

Thank you in advance

Best regards, 
--
Lam Nguyen, MSc.
Department of Pharmacology and Pharmacogenomics Research Center,
Inje University, Busan, Korea

Armando Stellato

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May 3, 2022, 5:23:36 AM5/3/22
to Lam Nguyen, Tiziano Lorenzetti, vocbench-user

Dear Lam,

 

VocBench’s backend platform, Semantic Turkey, has API for accessing and modifying its content.

 

http://semanticturkey.uniroma2.it/doc/user/first_access.jsf

http://semanticturkey.uniroma2.it/doc/user/web_api.jsf

 

You can write your own client in Python for using them.

 

Kind Regards,

 

Armando

 

 

Roland Wingerter

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May 3, 2022, 5:32:26 AM5/3/22
to vocbench-user
Hi Lam,

> Is it possible to connect VB ontology using python.

Check out the video "How to use Python and R with RDF data":

At 02:38 it shows how to connect to GraphDB running on local host.

See also the documentation at

Kind regards
Roland

Armando Stellato

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May 3, 2022, 6:57:04 AM5/3/22
to Roland Wingerter, vocbench-user

Dear all,

 

this is a more direct approach. The advantage in directly connecting to the triple store (GraphDB or RDF4J, whichever you are using) is that you can reuse some existing client for accessing specific tripe stores or at least compliant with the SPARQL protocol.

However, by using the ST API you would benefit from the full range of high-level API that can take care of all specific triples to be modified following a certain action. Also, passing by ST would be better in case history or validation are activated on the project.

 

In principle, both can be used. Let’s say that through-ST you benefit from all the existing logic of the platform and is generally safer. The other one is like tinkering under the hood, but you benefit from existing clients :-)

 

Kind Regards,


Armando

 

From: vocben...@googlegroups.com <vocben...@googlegroups.com> On Behalf Of Roland Wingerter
Sent: Tuesday, May 3, 2022 11:32 AM
To: vocbench-user <vocben...@googlegroups.com>
Subject: Re: [vocbench-user] ERROR: Query evaluation exception caught

 

Hi Lam,

Lam Nguyen

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May 3, 2022, 8:51:22 AM5/3/22
to vocbench-user
Dear Armando, 

Thank you for your information,
I searched this morning, but when I tried on the docker version, it raised an error. I don't know what exactly it is, I will show you tomorrow about that.

Best regards.

Lam Nguyen

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May 3, 2022, 8:54:41 AM5/3/22
to vocbench-user
Dear Roland,

Thanks for your sharing, 

I have viewed sparqlwrqpper, but I don't know how to set the SPARQL endpoint in Vocbench3.
I am sorry if it is a silly question. If you have documents or information, please share them with me. 

Many thanks again.

Best regards. 

Lam Nguyen

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May 3, 2022, 9:13:50 AM5/3/22
to vocbench-user
Dear Armando,

On more discussion on this issue. 

Currently, I would like to you graph database technique to develop our own knowledge graph database.
Since our data requires not only programming collection but also from the data curator team, this process requires a collaboration function as well as the user interface.
I have tried webprotege and Vocbench3, and each of software has its own advantages.
While webprotege is a lightweight editor, flexible editing, and has a comment function, Vocbench3 provides more functions about API connection and system integration (Although I don't know how to do it currently :)).

Anyways, my question is 
1. I would like to develop our knowledge base. The data building process requires both auto collection and data manual curation from other teams who are not IT-related members. So Vocbench3 is the right way for me to go.
2. Since our project will be connected with multiple RDF resources, one way I know is that we can load the RDF file to a new project, then use the alignment function to link the information. 
Are there any other ways to do it? and how we can manage those data when they are in production.

Anyways, thank you for sharing,

Sincerely,

Lam Nguyen

Roland Wingerter

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May 3, 2022, 1:54:50 PM5/3/22
to vocbench-user
Dear Lam,

> I don't know how to set the SPARQL endpoint in Vocbench3.
> If you have documents or information, please share them with me.

My command of Python is limited, but I followed the GraphDB example and it worked. Sorry, I wrongly assumed you are using GraphDB as triple store. Are you using the  RDF4J Native Store?

Kind regards
Roland




Armando Stellato

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May 4, 2022, 4:49:40 AM5/4/22
to Lam Nguyen, vocbench-user

Dear Lam,

 

A few notes first about the needs you mentioned in the paragraph before the questions. While not being a VB vs WebProtege thing, I just picked your list in order to check if other aspects you found in WebProtege can be easily covered in VB. While we can’t change the platform in a breeze, it’s important for us to get feedback or to show to you things you were not aware of.

 

Lightweight editor, flexible editing: I’m interested in this as, since you considered WebProtege, you are probably dealing with ontology and/or data (thesauri and lexicons are not supported by WebProtege). Is there anything that seems easier to be done?

Speaking about OWL, I find the Manchester editor quite easy and fast to be used, with syntax completion (not limited to the language, but extended to the same elements you are modeling), highlighting and toggle for syntactic/semantic checks. The rest: creating resources, linking them, should be pretty easy. Anyhow, if you find margin for improvement, we are all ears :-)

 

Comment function. You can go with two approaches:

  1. inData, using SKOS editorial notes (you can use SKOS even in a purely OWL file)
  2. outside the data, with connection to other collaboration tools. There are connectors to JIRA and to Freedcamp (more could follow in the next versions of VB3). See here: http://vocbench.uniroma2.it/doc/user/collab_platform.jsf

this is even better than just comments as you can keep discussions going on a separated platform, create issues of different types, mark them as in progress, resolved etc… You can do everything from within VocBench only using the connected tool as a backend or you can open links to the specific connected tool in order to work directly from there and use some tool-specific functionality

 

Now, to the explicit question you made:

 

The scenario you depicted is ok, but a precise answer depends on your specific case. If the resources are separated resources, the best thing is to keep them as separated projects and then align them.

For alignment, there are various solutions, from completely manual, passing through some automation to full automation and validation, see these links:

http://vocbench.uniroma2.it/doc/user/data_view.jsf#alignment_to_an_external_resource

http://vocbench.uniroma2.it/doc/user/alignment_validation.jsf

http://vocbench.uniroma2.it/doc/user/alignment_systems.jsf

However, if there’s a specific owl:import relation (e.g. one resource is an ontology and one another is a dataset importing that same ontology), then it is better that you manage the ontology in one project, periodically (I mean, when you freeze a new release) you export it, and then you owl:import it (http://vocbench.uniroma2.it/doc/user/namespaces_imports.jsf ) into your dataset. That is not linking indeed, it’s modeling (that is, your ontology resources are a vocabulary for describing the instance data in your dataset).

 

Another approach, if you want to keep things together, is that you put everything in one project. Let’s take for example the previous case of ontology O + dataset D and say that you have already a starting dataset and a starting ontology.

You create a project for dataset D (with baseuri/namespace for dataset D), then you owl:import the ontology O , so it will be imported in another graph.

Now, normally you will be able to edit only the dataset and the ontology will be read-only. However, you can switch the working graph on VB and change it to the one of the ontology, and then edit the ontology.

I personally prefer the first one, as I believe that, if the ontology has a life of its own and is possibly used by other datasets, it should have its own project and, in any case, you should change it periodically and not continuously. However, you might decide to follow this latter approach in a case of a more tight connection between ontology and data.

 

Kind Regards,

 

Armando

 

 

 

Lam Nguyen

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May 6, 2022, 5:10:44 AM5/6/22
to Armando Stellato, Tiziano Lorenzetti, vocbench-user
Dear Armando,

I followed the instruction from your links.

I could log in using the command below:

curl -X 'POST' \
'http://localhost:1979/semanticturkey/it.uniroma2.art.semanticturkey/st-core-services/Auth/login?email=mye...@gmail.com&password=mypassword&_spring_security_remember_me=true' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{}'

However, I could not list the projects:
curl -X 'POST' \
'http://127.0.0.1:1979/semanticturkey/it.uniroma2.art.semanticturkey/st-core-services/Projects/listProjects' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{}'

It raised an error: Access denied. You need to be logged in
I could not find any instructions about how to generate the token or something like that.

Update: I could find the JSESSIONID after login, then I could list the projects as your instruction.

However, how can I select a project to start with? It would be nice if we have more detailed documents about instructions. 
It would be very useful for us who are not developers and newbies like me. 
The explanation from your instruction seems not sufficient for me to follow. 

Best regards,

Lam Nguyen


Lam Nguyen

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May 6, 2022, 5:40:32 AM5/6/22
to Armando Stellato, Tiziano Lorenzetti, vocbench-user
Dear Armando, 

Updated about instruction document. 
I found your  javadoc page. It os very helpful for me at the moment, although I am not in java. Haha
Anyways. Thank you. 

Best  regards
--
Lam Nguyen Ph.D

Lead of Biomedical Information Center
Step

Armando Stellato

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May 6, 2022, 6:11:30 AM5/6/22
to Lam Nguyen, Tiziano Lorenzetti, vocbench-user

Dear Lam,

 

Eventually we will develop some tool to automatically produce client API docs for all the services in the platform. However, since currently there are hundreds of services, we described various ways to learn the API from available material (javadocs and source code, which are both available).

 

However, short recipe that can help you going directly to your needs and easily reproducible: run your browser and activate the devtools (e.g. CTRL+SHIFT+J on Chrome/Edge, CTRL+SHIFT+I on Firefox) , select “network”, then check all calls being done. You just need then to reproduce them when invoking your methods. Just remember each time you run a batch with various calls to preempt the login first (as you have already learned).

 

Kind Regards,

 

Armando

 

 

 

From: vocben...@googlegroups.com <vocben...@googlegroups.com> On Behalf Of Lam Nguyen
Sent: Friday, May 6, 2022 11:10 AM
To: Armando Stellato <stel...@uniroma2.it>
Cc: Tiziano Lorenzetti <tiziano.l...@gmail.com>; vocbench-user <vocben...@googlegroups.com>
Subject: {Disarmed} Re: [vocbench-user] ERROR: Query evaluation exception caught

 

Dear Armando,

 

I followed the instruction from your links.

 

I could log in using the command below:

 

curl -X 'POST' \
'http://localhost:1979/semanticturkey/it.uniroma2.art.semanticturkey/st-core-services/Auth/login?email=mye...@gmail.com&password=mypassword&_spring_security_remember_me=true' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{}'

 

However, I could not list the projects:

Lam Nguyen

unread,
May 6, 2022, 7:38:57 PM5/6/22
to vocbench-user
Dear Roland,

It is fine, thank you for your support.
Since I am a very newbie in this field, I am reviewing and studying each of them. 
I am working on Vocbench3, but it seems that I used the native store.

Best regards.
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