remove isAmount from reactio

hetalang · Jan 25, 2024 · 2245823 · 2245823
1 parent f599d0e
commit 2245823
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Showing 7 changed files with 6 additions and 16 deletions.
diff --git a/TODO.md b/TODO.md
@@ -42,7 +42,6 @@
 - checking legal functions inside Expressions and functionDefinition
 - `#defineFunction`: different exports, functionDef vs units
 - write reusable `Build` class
-- remove `isAmount` properties from `@Reaction`
 
 ## ideas
 

diff --git a/src/another-xlsx-export/index.js b/src/another-xlsx-export/index.js
@@ -59,7 +59,6 @@ class AnotherXLSXExport extends XLSXExport {
         .map((_q) => {
           //q['#'] = counter++;
           let q = {st: 'r', ..._q};
-          if (q.isAmount !== false) q.compartment = 'no';
           delete q.class;
           delete q.units;
           delete q.units2;

diff --git a/src/core/reaction.js b/src/core/reaction.js
@@ -14,7 +14,6 @@ const { UnitTerm } = require('./unit-term');
 class Reaction extends Process {
   constructor(isCore = false){
     super(isCore);
-    this.isAmount = true;
     this.modifiers = [];
   }
   merge(q = {}){
@@ -35,7 +34,6 @@ class Reaction extends Process {
       }
 
       if (q.compartment !== undefined) this.compartment = q.compartment;
-      if (q.isAmount !== undefined) this.isAmount = !!q.isAmount;
     }
 
     return this;
@@ -46,10 +44,9 @@ class Reaction extends Process {
   clone(){
     let clonedComponent = super.clone();
 
-    if (this.modifiers.length > 0)
+    if (this.modifiers.length > 0) {
       clonedComponent.modifiers = this.modifiers.map((modifier) => modifier.clone());
-    if (typeof this.isAmount !== 'undefined')
-      clonedComponent.isAmount = this.isAmount;
+    }
 
     return clonedComponent;
   }
@@ -62,7 +59,6 @@ class Reaction extends Process {
     }
 
     if (this.compartment !== undefined) res.compartment = this.compartment;
-    if (this.isAmount !== true) res.isAmount = this.isAmount;
 
     return res;
   }

diff --git a/src/core/species.js b/src/core/species.js
@@ -36,8 +36,8 @@ class Species extends Record {
   }
   toQ(options = {}){
     let res = super.toQ(options);
-    if(this.compartment) res.compartment = this.compartment;
-    if(this.isAmount) res.isAmount = this.isAmount;
+    if (this.compartment) res.compartment = this.compartment;
+    if (this.isAmount) res.isAmount = this.isAmount;
     return res;
   }
   unitsSBML(){

diff --git a/src/heta.json-schema.json b/src/heta.json-schema.json
@@ -178,10 +178,6 @@
               { "$ref": "#/definitions/ID" }
             ]
           }
-        },
-        "isAmount": { "enum": [true, false, 1, 0] },
-        "compartment": {
-          "$ref": "#/definitions/ID"
         }
       },
       "errorMessage": {

diff --git a/src/templates/dbsolve-model.slv.njk b/src/templates/dbsolve-model.slv.njk
@@ -1,6 +1,6 @@
 {% macro diff(backReferences = []) -%}
 {% for br in backReferences|exclude2('stoichiometry', undefined) -%}
-{% if br.stoichiometry > 0 and not loop.first %}+{% endif %}{{ br.stoichiometry + '*'}}{{ br.process }}{{ '' if br._process_.isAmount!==false else '*' + br._process_.compartment }}
+{% if br.stoichiometry > 0 and not loop.first %}+{% endif %}{{ br.stoichiometry + '*'}}{{ br.process }}
 {%- endfor %}
 {%- endmacro %}
 {%- set compartments = population.selectByClassName('Compartment') %}

diff --git a/src/templates/slv-blocks-template.slv.njk b/src/templates/slv-blocks-template.slv.njk
@@ -58,7 +58,7 @@ default_compartment_ = 1; // {units: UL} This is fake compartment to support com
 =============================== RHS ================================
 {% macro diff(backReferences=[]) -%}
 {% for br in backReferences|exclude2('stoichiometry', undefined) -%}
-{% if br.stoichiometry>0 and not loop.first %}+{% endif %}{{ br.stoichiometry + '*'}}{{ br.process }}{{ '' if br._process_.isAmount!==false else '*' + br._process_.compartment }}
+{% if br.stoichiometry>0 and not loop.first %}+{% endif %}{{ br.stoichiometry + '*'}}{{ br.process }}
 {%- endfor %}
 {%- endmacro %}
 {% block rhs %}