feat: stratification related support functions (#1356)

packages/client/hmi-client/src/model-representation/petrinet/petrinet-service.ts

@@ -1,6 +1,7 @@
 import _ from 'lodash';
+import API from '@/api/api';
 import { IGraph } from '@graph-scaffolder/types';
-import { PetriNetModel, Model, PetriNetTransition } from '@/types/Types';
+import { PetriNetModel, Model, PetriNetTransition, TypingSemantics } from '@/types/Types';
 import { PetriNet } from '@/petrinet/petrinet-service';
 
 export interface NodeData {
@@ -259,6 +260,8 @@ export const removeTransition = (amr: Model, id: string) => {
  }
 };
 
+// Update a transition's expression and expression_mathml fields based on
+// mass-kinetics
 export const updateRateExpression = (amr: Model, transition: PetriNetTransition) => {
  const rate = amr.semantics?.ode.rates.find((d) => d.target === transition.id);
  if (!rate) return;
@@ -360,3 +363,33 @@ export const updateTransitioneId = (amr: Model, id: string, newId: string) => {
  if (!rate) return;
  rate.target = newId;
 };
+
+// Replace typing semantics
+export const addTyping = (amr: Model, typing: TypingSemantics) => {
+ if (amr.semantics) {
+ amr.semantics.typing = typing;
+ }
+};
+
+// Add a reflexive transition loop to the state
+// This is a special type of addTransition that creates a self loop
+export const addReflexives = (amr: Model, stateId: string, reflexiveId: string) => {
+ addTransition(amr, reflexiveId, reflexiveId);
+ const transition = (amr.model as PetriNetModel).transitions.find((t) => t.id === reflexiveId);
+ if (transition) {
+ transition.input = [stateId];
+ transition.output = [stateId];
+ }
+};
+
+export const mergeMetadata = (amr: Model, amrOld: Model) => {
+ console.log(amr, amrOld);
+};
+
+export const stratify = async (baseAMR: Model, fluxAMR: Model) => {
+ const response = await API.post('/modeling-request/stratify', {
+ baseModel: baseAMR,
+ fluxModel: fluxAMR
+ });
+ return response.data as Model;
+};

packages/client/hmi-client/src/types/Types.ts

@@ -225,7 +225,7 @@ export interface PetriNetTransition {
  id: string;
  input: string[];
  output: string[];
- grounding: ModelGrounding;
+ grounding?: ModelGrounding;
  properties: PetriNetTransitionProperties;
 }
 
@@ -311,8 +311,8 @@ export interface ModelExpression {
 
 export interface PetriNetTransitionProperties {
  name: string;
- grounding: ModelGrounding;
- rate: ModelExpression;
+ description: string;
+ grounding?: ModelGrounding;
 }
 
 export interface Extraction {

packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/modelparts/semantics/TypingSemantics.java

@@ -11,9 +11,7 @@
 @Accessors(chain = true)
 public class TypingSemantics {
 
- @JsonProperty("type_system")
- private TypeSystem typeSystem;
+ private TypeSystem type_system;
 
- @JsonProperty("type_map")
- private List<List<String>> typeMap;
+ private List<List<String>> type_map;
 }

packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/petrinet/PetriNetTransition.java

@@ -1,6 +1,7 @@
 package software.uncharted.terarium.hmiserver.models.dataservice.petrinet;
 
 import software.uncharted.terarium.hmiserver.models.dataservice.modelparts.ModelGrounding;
+import software.uncharted.terarium.hmiserver.annotations.TSOptional;
 
 import lombok.Data;
 import lombok.experimental.Accessors;
@@ -13,7 +14,10 @@ public class PetriNetTransition {
  private String id;
  private List<String> input;
  private List<String> output;
+
+ @TSOptional
  private ModelGrounding grounding;
+
  private PetriNetTransitionProperties properties;
 }
 

packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/models/dataservice/petrinet/PetriNetTransitionProperties.java

@@ -5,12 +5,15 @@
 
 import lombok.Data;
 import lombok.experimental.Accessors;
+import software.uncharted.terarium.hmiserver.annotations.TSOptional;
 
 @Data
 @Accessors(chain = true)
 public class PetriNetTransitionProperties {
  private String name;
+ private String description;
+
+ @TSOptional
  private ModelGrounding grounding;
- private ModelExpression rate;
 }
 

packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/proxies/modelservice/ModelServiceProxy.java

@@ -17,4 +17,12 @@ public interface ModelServiceProxy {
  Response petrinetToLatex(
  PetriNet content
  );
+
+ @POST
+ @Path("/api/stratify")
+ @Consumes(MediaType.APPLICATION_JSON)
+ Response stratify(
+ Object baseModel,
+ Object fluModel
+ );
 }

packages/services/hmi-server/src/main/java/software/uncharted/terarium/hmiserver/resources/modelservice/ModelingRequestResource.java

@@ -0,0 +1,35 @@
+package software.uncharted.terarium.hmiserver.resources.modelservice;
+
+import org.eclipse.microprofile.openapi.annotations.tags.Tag;
+import org.eclipse.microprofile.rest.client.inject.RestClient;
+
+import javax.ws.rs.*;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+
+
+import software.uncharted.terarium.hmiserver.proxies.modelservice.ModelServiceProxy;
+
+
+@Path("/api/modeling-request")
+@Produces(MediaType.APPLICATION_JSON)
+@Consumes(MediaType.APPLICATION_JSON)
+@Tag(name = "Modeling Service REST Endpoint")
+public class ModelingRequestResource {
+
+ @RestClient
+ ModelServiceProxy modelServiceProxy;
+
+ @POST
+ @Path("/stratify")
+ @Produces(MediaType.APPLICATION_JSON)
+ @Consumes(MediaType.APPLICATION_JSON)
+ @Tag(name = "Stratify two AMR models together")
+ public Object stratify(
+ final Object baseModel,
+ final Object fluxModel
+ ) {
+ return modelServiceProxy.stratify(baseModel, fluxModel);
+ }
+}
+