feat: adopting MMT part 1 - diagrams

[mwdchang]

Summary

This PR most changes tera-model-diagram and related components to adopt MMT formats

• No longer generating model previews via beaker-kernel
• Clean up petrinet related services and utilities, a 2nd pass will be needed to move things into their proper folders for functions that are reused
• Fix and augment existing MIRA parsing features
• Clean up tera-model-diagram in general, there are a decent chunk of things sitting around not being used

"model-representation/service" serves as the main entry-point for getting the renderer

Note: there may be a few edge cases where the rendering breaks, because we have never fully tested regnet/stockflow.

Controller:

Regnet:

Petri-stratafied

Petri not-stratified

Testing

• Model diagrams for regnet/stockflow will be rendered in-house

[YohannParis]

Tang2020.json
I get the Stratified colours on this non-stratified PetriNet and others

[YohannParis]

I get 500 using the following request to api/mira/amr-to-mmt

RegNet request

{"id":"e24df5ff-0981-4949-8ba8-d175fd318167","createdOn":"2024-03-13T18:36:49.027+00:00","updatedOn":"2024-03-13T18:37:17.965+00:00","temporary":false,"publicAsset":false,"header":{"name":"Regnet mathml model","description":"This is a Regnet model from mathml equations","schema":"https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.1/regnet/regnet_schema.json","schema_name":"regnet","model_version":"0.1"},"model":{"vertices":[{"id":"I","name":"I","initial":"I0","rate_constant":"γ","sign":true},{"id":"R","name":"R","initial":"R0"},{"id":"S","name":"S","initial":"S0"}],"edges":[{"id":"t0","source":["I","S"],"target":["I","I"],"sign":true,"properties":{"name":"β"}},{"id":"t1","source":["I"],"target":["R"],"sign":true,"properties":{"name":"γ"}}],"parameters":[{"id":"I","name":"I","description":"The total I population at timestep 0"},{"id":"R","name":"R","description":"The total R population at timestep 0"},{"id":"S","name":"S","description":"The total S population at timestep 0"},{"id":"β","name":"β","description":"β rate"},{"id":"γ","name":"γ","description":"γ rate"}]},"metadata":{}}

Response

{"timestamp":"2024-03-13T18:37:19.260+00:00","status":500,"error":"Internal Server Error","trace":"org.springframework.web.server.ResponseStatusException: 500 INTERNAL_SERVER_ERROR \"Unable to dispatch task request\"\n\tat software.uncharted.terarium.hmiserver.controller.mira.MiraController.convertAMRtoMMT(MiraController.java:106)\n\tat java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:578)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:196)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)\n\tat org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:751)\n\tat org.springframework.security.access.intercept.aopalliance.MethodSecurityInterceptor.invoke(MethodSecurityInterceptor.java:67)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:184)\n\tat org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:751)\n\tat org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:703)\n\tat software.uncharted.terarium.hmiserver.controller.mira.MiraController$$SpringCGLIB$$0.convertAMRtoMMT(<generated>)\n\tat java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:578)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)\n\tat org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:150)\n\tat org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:118)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:884)\n\tat org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797)\n\tat org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87)\n\tat org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1081)\n\tat org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:974)\n\tat org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1011)\n\tat org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:914)\n\tat jakarta.servlet.http.HttpServlet.service(HttpServlet.java:590)\n\tat org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:885)\n\tat jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:205)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.springframework.security.web.FilterChainProxy.lambda$doFilterInternal$3(FilterChainProxy.java:231)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$FilterObservation$SimpleFilterObservation.lambda$wrap$1(ObservationFilterChainDecorator.java:479)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$AroundFilterObservation$SimpleAroundFilterObservation.lambda$wrap$1(ObservationFilterChainDecorator.java:340)\n\tat org.springframework.security.web.ObservationFilterChainDecorator.lambda$wrapSecured$0(ObservationFilterChainDecorator.java:82)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:128)\n\tat org.springframework.security.web.access.intercept.AuthorizationFilter.doFilter(AuthorizationFilter.java:100)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:126)\n\tat org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:120)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:131)\n\tat org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:85)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:100)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:179)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.oauth2.server.resource.web.authentication.BearerTokenAuthenticationFilter.doFilterInternal(BearerTokenAuthenticationFilter.java:145)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat software.uncharted.terarium.hmiserver.filters.ServiceRequestFilter.doFilter(ServiceRequestFilter.java:72)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:107)\n\tat org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:93)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:90)\n\tat org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:75)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.context.SecurityContextHolderFilter.doFilter(SecurityContextHolderFilter.java:82)\n\tat org.springframework.security.web.context.SecurityContextHolderFilter.doFilter(SecurityContextHolderFilter.java:69)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:62)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:227)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.session.DisableEncodeUrlFilter.doFilterInternal(DisableEncodeUrlFilter.java:42)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.wrapFilter(ObservationFilterChainDecorator.java:240)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$AroundFilterObservation$SimpleAroundFilterObservation.lambda$wrap$0(ObservationFilterChainDecorator.java:323)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$ObservationFilter.doFilter(ObservationFilterChainDecorator.java:224)\n\tat org.springframework.security.web.ObservationFilterChainDecorator$VirtualFilterChain.doFilter(ObservationFilterChainDecorator.java:137)\n\tat org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:233)\n\tat org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:191)\n\tat org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:352)\n\tat org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:268)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.springframework.web.filter.ServerHttpObservationFilter.doFilterInternal(ServerHttpObservationFilter.java:109)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)\n\tat org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:116)\n\tat org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:174)\n\tat org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:149)\n\tat org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:167)\n\tat org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90)\n\tat org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:482)\n\tat org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:115)\n\tat org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93)\n\tat org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)\n\tat org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:340)\n\tat org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:391)\n\tat org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63)\n\tat org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:896)\n\tat org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1744)\n\tat org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52)\n\tat org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)\n\tat org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)\n\tat org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)\n\tat java.base/java.lang.Thread.run(Thread.java:1589)\n","message":"Unable to dispatch task request","path":"/mira/amr-to-mmt"}

[YohannParis]

Great cleaning