use compartment for @reaction in DOT

hetalang · Dec 22, 2023 · e724667 · e724667
1 parent a0b5af8
commit e724667
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/TODO.md b/TODO.md
@@ -42,7 +42,7 @@
 - checking legal functions inside Expressions and functionDefinition
 - `#defineFunction`: circular dependences within functions, internal functions, different exports, functionDef vs units
 - write reusable `Build` class
-- remove `isAmount`, `compartment` properties from `@Reaction`
+- remove `isAmount` properties from `@Reaction`
 
 ## ideas
 

diff --git a/src/dot-export/namespace.js b/src/dot-export/namespace.js
@@ -10,13 +10,15 @@ Namespace.prototype.getDotImage = function() {
       let substrates = proc.actors.filter((x) => x.stoichiometry < 0);
       // push records
       proc.actors.forEach((actor) => {
-        let record = this.get(actor.target) || { id: actor.target }; // use fake record
+        let record = this.get(actor.target) || { id: actor.target }; // use target record or fake record for abstract NS
         let compartmentId = record.compartment || '_';
         clustersDict[compartmentId]?.push(record) || (clustersDict[compartmentId] = [record]);
       });
       // push process
-      let compartmentOfFirstSubstrate = this.get(substrates[0]?.target)?.compartment || '_';
-      clustersDict[compartmentOfFirstSubstrate]?.push(proc);
+      let compartmentOfReaction = proc.compartment // use explicit compartment, first substrate compartment, or empty
+        || this.get(substrates[0]?.target)?.compartment 
+        || '_';
+      clustersDict[compartmentOfReaction]?.push(proc);
     });
   /* display all records
   this.selectByInstanceOf('Record')