multiple request for conversion to SBML can end up with 500 result
The identified root cause is this: https://github.com/sbmlteam/jsbml/issues/195
exception might look like:
2020-01-31 15:23:13,489 ERROR [http-nio-8080-exec-3] (BaseController.java:55) - lcsb.mapviewer.converter.ConverterException: lcsb.mapviewer.model.map.InconsistentModelException: [StateTransitionReaction re8] Problem with exporting bioEntity
lcsb.mapviewer.converter.ConverterException: lcsb.mapviewer.model.map.InconsistentModelException: [StateTransitionReaction re8] Problem with exporting bioEntity
at lcsb.mapviewer.converter.model.sbml.SbmlParser.model2String(SbmlParser.java:133) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.Converter.model2InputStream(Converter.java:75) ~[converter-1.0.jar:?]
at lcsb.mapviewer.api.projects.models.ModelRestImpl.getModelAsModelFile(ModelRestImpl.java:225) ~[rest-api-1.0.jar:?]
at lcsb.mapviewer.api.projects.models.ModelRestImpl$$FastClassBySpringCGLIB$$80015a71.invoke(<generated>) ~[rest-api-1.0.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.projects.models.ModelRestImpl$$EnhancerBySpringCGLIB$$7752af30.getModelAsModelFile(<generated>) ~[rest-api-1.0.jar:?]
at lcsb.mapviewer.api.projects.models.ModelController.getModelAsModelFile(ModelController.java:116) ~[rest-api-1.0.jar:?]
at lcsb.mapviewer.api.projects.models.ModelController$$FastClassBySpringCGLIB$$3e1e72b9.invoke(<generated>) ~[rest-api-1.0.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$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:746) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:69) ~[spring-security-core-5.0.8.RELEASE.jar:5.0.8.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:185) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:688) ~[spring-aop-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at lcsb.mapviewer.api.projects.models.ModelController$$EnhancerBySpringCGLIB$$ea5b7066.getModelAsModelFile(<generated>) ~[rest-api-1.0.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
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.doGet(FrameworkServlet.java:866) [spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
at javax.servlet.http.HttpServlet.service(HttpServlet.java:635) [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) [servlet-api.jar:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) [catalina.jar:8.5.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [catalina.jar:8.5.41]
at lcsb.mapviewer.web.bean.utils.XFrameFilter.doFilter(XFrameFilter.java:37) [classes/:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [catalina.jar:8.5.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [catalina.jar:8.5.41]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat-websocket.jar:8.5.41]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) [catalina.jar:8.5.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [catalina.jar:8.5.41]
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) [catalina.jar:8.5.41]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) [catalina.jar:8.5.41]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:199) [catalina.jar:8.5.41]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) [catalina.jar:8.5.41]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493) [catalina.jar:8.5.41]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:137) [catalina.jar:8.5.41]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) [catalina.jar:8.5.41]
at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:660) [catalina.jar:8.5.41]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) [catalina.jar:8.5.41]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) [catalina.jar:8.5.41]
at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:798) [tomcat-coyote.jar:8.5.41]
at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) [tomcat-coyote.jar:8.5.41]
at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:808) [tomcat-coyote.jar:8.5.41]
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498) [tomcat-coyote.jar:8.5.41]
at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat-coyote.jar:8.5.41]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-util.jar:8.5.41]
at java.lang.Thread.run(Thread.java:834) [?:?]
Caused by: lcsb.mapviewer.model.map.InconsistentModelException: [StateTransitionReaction re8] Problem with exporting bioEntity
at lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter.exportElements(SbmlBioEntityExporter.java:84) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toSbmlDocument(SbmlExporter.java:124) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toXml(SbmlExporter.java:50) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlParser.model2String(SbmlParser.java:131) ~[converter-sbml-1.0.jar:?]
... 100 more
Caused by: java.lang.NullPointerException
at org.sbml.jsbml.Annotation.setNonRDFAnnotation(Annotation.java:871) ~[jsbml-core-1.4.jar:?]
at org.sbml.jsbml.AbstractSBase.setAnnotation(AbstractSBase.java:2402) ~[jsbml-core-1.4.jar:?]
at org.sbml.jsbml.AbstractSBase.setAnnotation(AbstractSBase.java:2391) ~[jsbml-core-1.4.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter.getSbmlElement(SbmlBioEntityExporter.java:126) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter.exportElements(SbmlBioEntityExporter.java:77) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toSbmlDocument(SbmlExporter.java:124) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlExporter.toXml(SbmlExporter.java:50) ~[converter-sbml-1.0.jar:?]
at lcsb.mapviewer.converter.model.sbml.SbmlParser.model2String(SbmlParser.java:131) ~[converter-sbml-1.0.jar:?]
... 100 more