problem with jsbml
Taken from minerva-service:
2021-11-15 18:50:17,085 ERROR [http-nio-8080-exec-10] (BaseController.java:64) - lcsb.mapviewer.converter.ConverterException: lcsb.mapviewer.model.map.InconsistentModelException: [Compartment default] Problem with exporting bioEntity
lcsb.mapviewer.converter.ConverterException: lcsb.mapviewer.model.map.InconsistentModelException: [Compartment default] Problem with exporting bioEntity
at lcsb.mapviewer.converter.model.sbml.SbmlParser.model2String(SbmlParser.java:133) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.Converter.model2InputStream(Converter.java:75) ~[converter-16.0.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl.convert(ConvertRestImpl.java:66) ~[rest-api-16.0.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl$$FastClassBySpringCGLIB$$c6591b50.invoke(<generated>) ~[rest-api-16.0.0.jar:?]
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) ~[spring-core-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:746) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:688) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at lcsb.mapviewer.api.convert.ConvertRestImpl$$EnhancerBySpringCGLIB$$9da6ac33.convert(<generated>) ~[rest-api-16.0.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertController.convertInput(ConvertController.java:41) ~[rest-api-16.0.0.jar:?]
at sun.reflect.GeneratedMethodAccessor184.invoke(Unknown Source) ~[?:?]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_292]
at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_292]
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:891) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:974) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:877) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:661) [tomcat8-servlet-api.jar:?]
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:851) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) [tomcat8-servlet-api.jar:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:37) [classes/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat8-websocket-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:170) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at lcsb.mapviewer.web.bean.utils.CORSFilter.doFilter(CORSFilter.java:43) [classes/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at lcsb.mapviewer.web.bean.utils.CacheFilter.doFilter(CacheFilter.java:38) [classes/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:37) [classes/:?]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:200) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:66) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178) [spring-security-web-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:357) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:270) [spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:200) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:660) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) [tomcat8-catalina-8.5.39.jar:8.5.39]
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:798) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498) [tomcat8-coyote-8.5.39.jar:8.5.39]
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat8-coyote-8.5.39.jar:8.5.39]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_292]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_292]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat8-util-8.5.39.jar:8.5.39]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_292]
Caused by: lcsb.mapviewer.model.map.InconsistentModelException: [Compartment default] Problem with exporting bioEntity
at lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter.exportElements(SbmlBioEntityExporter.java:96) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toSbmlDocument(SbmlExporter.java:123) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toXml(SbmlExporter.java:50) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlParser.model2String(SbmlParser.java:131) ~[converter-sbml-16.0.0.jar:?]
... 91 more
Caused by: java.lang.IllegalArgumentException: Cannot register compartmentGlyph.
at org.sbml.jsbml.AbstractSBase.registerChild(AbstractSBase.java:2220) ~[jsbml-core-1.5.jar:?]
at org.sbml.jsbml.ListOf.add(ListOf.java:444) ~[jsbml-core-1.5.jar:?]
at org.sbml.jsbml.ext.layout.Layout.addCompartmentGlyph(Layout.java:166) ~[jsbml-layout-1.5.jar:?]
at org.sbml.jsbml.ext.layout.Layout.createCompartmentGlyph(Layout.java:301) ~[jsbml-layout-1.5.jar:?]
at lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter.createElementGlyph(SbmlCompartmentExporter.java:90) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter.createGlyph(SbmlBioEntityExporter.java:149) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter.exportElements(SbmlBioEntityExporter.java:93) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toSbmlDocument(SbmlExporter.java:123) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toXml(SbmlExporter.java:50) ~[converter-sbml-16.0.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlParser.model2String(SbmlParser.java:131) ~[converter-sbml-16.0.0.jar:?]
... 91 more