Error when exporting an SBML file to graphics
When trying to convert the attached file to an image with the attached script, I get an ArrayIndexOutOfBoundException when drawing the reaction re1422_406. The issue might be that all the species share the position.
2019-06-17 12:46:10,921 ERROR [http-bio-8080-exec-8] (BaseController.java:47) - lcsb.mapviewer.converter.graphics.DrawingException: [DissociationReaction reaction_glyph_0__re1422__rg_re1422_406] Problem with drawing element.
lcsb.mapviewer.converter.graphics.DrawingException: [DissociationReaction reaction_glyph_0__re1422__rg_re1422_406] Problem with drawing element.
at lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl.draw(BioEntityConverterImpl.java:198) ~[converter-graphics-1.0.jar:?]
at lcsb.mapviewer.converter.graphics.AbstractImageGenerator.drawReaction(AbstractImageGenerator.java:847) ~[converter-graphics-1.0.jar:?]
at lcsb.mapviewer.converter.graphics.AbstractImageGenerator.draw(AbstractImageGenerator.java:718) ~[converter-graphics-1.0.jar:?]
at lcsb.mapviewer.converter.graphics.AbstractImageGenerator.saveToOutputStream(AbstractImageGenerator.java:935) ~[converter-graphics-1.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl.converToImage(ConvertRestImpl.java:68) ~[rest-api-1.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl.converToImage(ConvertRestImpl.java:78) ~[rest-api-1.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertRestImpl$$FastClassBySpringCGLIB$$c6591b50.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.convert.ConvertRestImpl$$EnhancerBySpringCGLIB$$e582f06f.converToImage(<generated>) ~[rest-api-1.0.jar:?]
at lcsb.mapviewer.api.convert.ConvertController.convertInputToImage(ConvertController.java:71) ~[rest-api-1.0.jar:?]
at sun.reflect.GeneratedMethodAccessor94.invoke(Unknown Source) ~[?:?]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_181]
at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_181]
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:650) [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:731) [servlet-api.jar:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.90]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.90]
at lcsb.mapviewer.web.bean.utils.ApiAccessControlFilter.doFilter(ApiAccessControlFilter.java:42) [ApiAccessControlFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.90]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.90]
at lcsb.mapviewer.web.bean.utils.JsfAjaxAccessControlAllowFilter.doFilter(JsfAjaxAccessControlAllowFilter.java:47) [JsfAjaxAccessControlAllowFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.90]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.90]
at lcsb.mapviewer.web.bean.utils.XFrameAccessControlFilter.doFilter(XFrameAccessControlFilter.java:54) [XFrameAccessControlFilter.class:?]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.90]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.90]
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.90]
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.90]
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.90]
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219) [catalina.jar:7.0.90]
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110) [catalina.jar:7.0.90]
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:494) [catalina.jar:7.0.90]
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) [catalina.jar:7.0.90]
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104) [catalina.jar:7.0.90]
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:1025) [catalina.jar:7.0.90]
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.90]
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445) [catalina.jar:7.0.90]
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1136) [tomcat-coyote.jar:7.0.90]
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637) [tomcat-coyote.jar:7.0.90]
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) [tomcat-coyote.jar:7.0.90]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_181]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_181]
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.90]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_181]
Caused by: java.lang.ArrayIndexOutOfBoundsException