support in simbio export

hetalang · Jun 20, 2024 · 1ea6b8d · 1ea6b8d
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diff --git a/export-formats.md b/export-formats.md
@@ -413,7 +413,7 @@ Each namespace in separate file.
 |Const: `Infinity`, `NaN`                                |- |- |+ |+ |+ |+ |+ |+ |+ |na 
 |`@Scenario` support                                     |- |- |- |- |- |- |- |+ |+ |na
 |`@Record {ss: true, ...}`                               |- |- |+ |- |- |- |- |+ |+ |na
-|`#defineFunction`, (sub) means substitution             |+ (sub) |+ (sub) |+ |+ |+ |- |+ |+ |+ |na
+|`#defineFunction`, (sub) means substitution             |+(sub) |+(sub) |+ |+(sub) |+ |+(sub) |+ |+ |+ |na
 
 ## Math expressions conversions
 

diff --git a/src/julia-export/expression.js b/src/julia-export/expression.js
@@ -1,6 +1,8 @@
 const { Expression } = require('../core/expression');
 
-Expression.prototype.toJuliaString = function(){
+Expression.prototype.toJuliaString = function(substituteByDefinitions) {
+  let tree = substituteByDefinitions ? this.substituteByDefinitions().exprParsed : this.exprParsed;
+
   let juliaStringHandler = (node, options) => {
     if(node.type==='ConstantNode' && Number.isInteger(node.value)){
       return node.value.toExponential(); // to display 6 => 6e0; 6e23 => 6e+23
@@ -134,12 +136,11 @@ Expression.prototype.toJuliaString = function(){
     }
   };
 
-  return this.exprParsed
-    .toString({
-      parenthesis: 'keep',
-      implicit: 'show',
-      handler: juliaStringHandler
-    });
+  return tree.toString({
+    parenthesis: 'keep',
+    implicit: 'show',
+    handler: juliaStringHandler
+  });
 };
 
 module.exports = Expression;
diff --git a/src/matlab-export/expression.js b/src/matlab-export/expression.js
@@ -1,6 +1,8 @@
 const { Expression } = require('../core/expression');
 
-Expression.prototype.toMatlabString = function(){
+Expression.prototype.toMatlabString = function(substituteByDefinitions = true) {
+  let tree = substituteByDefinitions ? this.substituteByDefinitions().exprParsed : this.exprParsed;
+
   let matlabStringHandler = (node, options) => {
     if (node.type==='FunctionNode' && node.fn.name==='pow') {
       return `power(${node.args[0].toString(options)}, ${node.args[1].toString(options)})`;
@@ -95,12 +97,11 @@ Expression.prototype.toMatlabString = function(){
     }
   };
 
-  return this.exprParsed
-    .toString({
-      parenthesis: 'keep',
-      implicit: 'show',   
-      handler: matlabStringHandler
-    });
+  return tree.toString({
+    parenthesis: 'keep',
+    implicit: 'show',   
+    handler: matlabStringHandler
+  });
 };
 
 module.exports = Expression;
diff --git a/src/simbio-export/index.js b/src/simbio-export/index.js
@@ -31,16 +31,8 @@ class SimbioExport extends AbstractExport {
     return true;
   }
   // return text for all namespaces
-  makeText(){
-    let logger = this._container.logger;
-
-    // display that function definition is not supported
-    let userDefinedFunctions = [...this._container.functionDefStorage]
-      .filter(([id, functionDef]) => !functionDef.isCore)
-      .map(([id, functionDef]) => id);
-    if (userDefinedFunctions.length > 0) {
-      logger.warn(`User defined functions: ${userDefinedFunctions.join(', ')} are presented in platform but not supported by Simbio export.`);
-    }
+  makeText() {
+    //let logger = this._container.logger;
 
     let results = this.selectedNamespaces().map(([spaceName, ns]) => {
 

diff --git a/src/templates/julia-model.jl.njk b/src/templates/julia-model.jl.njk
@@ -19,7 +19,7 @@
 __platform__ = (function()
 {% for fd in functionDefArray %}
 function {{ fd.id }}({% for a in fd.arguments %}{{ a }}, {% endfor %}__args__...)
-  return {{ fd.math.toJuliaString() }}
+  return {{ fd.math.toJuliaString(false) }}
 end
 {%- endfor %}
 
@@ -85,9 +85,9 @@ function {{ id }}_init_func_(__constants__)
     {%- endfor %}
     {% for record in img.initRecords -%}
     {% if record.isRule -%}
-    {{ record.id }} = {{ record.getAssignment('ode_').translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.getAssignment('ode_').translateSymbol(img.pTranslator).toJuliaString(false) }}
     {%- else -%}
-    {{ record.id }} = {{ record.getAssignment('start_').translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.getAssignment('start_').translateSymbol(img.pTranslator).toJuliaString(false) }}
     {%- endif %}
     {% endfor %}
     # save results
@@ -132,7 +132,7 @@ function {{ id }}_ode_func_(__du__, __u__, __p__, t)
     {%- endfor %}
     {% for record in img.odeRules %}
     {%- if record.isRule -%}
-    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString(false) }}
     {% elif record.instanceOf('Species') and not record.isAmount -%}
     {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
     {% endif -%}
@@ -181,7 +181,7 @@ function {{ id }}_saving_generator_(__outputIds__::Vector{Symbol})
         {%- endfor %}
         {% for record in img.extendedRuleRecords %}
         {%- if record.isRule -%}
-        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString() }}
+        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString(false) }}
         {% elif record.instanceOf('Species') and not record.isAmount -%}
         {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
         {% endif -%}
@@ -231,13 +231,13 @@ function {{ id }}_{{ event.switcher.id }}_condition_func_(__u__, t, __integrator
     {%- endfor %}
     {% for record in event.triggerRules %}
     {%- if record.isRule -%}
-    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString(false) }}
     {% elif record.instanceOf('Species') and not record.isAmount -%}
     {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
     {% endif -%}
     {% endfor %}
 
-    return ({{ event.switcher.trigger.translateSymbol(img.pTranslator).toJuliaString() if event.switcher.trigger is defined else 'false' }}) ? 1 : -1
+    return ({{ event.switcher.trigger.translateSymbol(img.pTranslator).toJuliaString(false) if event.switcher.trigger is defined else 'false' }}) ? 1 : -1
 end
 {%- endfor %}
 
@@ -257,13 +257,13 @@ function {{ id }}_{{ event.switcher.id }}_condition_func_(__u__, t, __integrator
     {%- endfor %}
     {% for record in event.triggerRules %}
     {%- if record.isRule -%}
-    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString(false) }}
     {% elif record.instanceOf('Species') and not record.isAmount -%}
     {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
     {% endif -%}
     {% endfor %}
 
-    return {{ event.switcher.trigger.translateSymbol(img.pTranslator).toJuliaString() if event.switcher.trigger is defined else '-1' }}
+    return {{ event.switcher.trigger.translateSymbol(img.pTranslator).toJuliaString(false) if event.switcher.trigger is defined else '-1' }}
 end
 {%- endfor %}
 
@@ -285,13 +285,13 @@ function {{ id }}_{{ event.switcher.id }}_condition_func_(__u__, t, __integrator
     {%- endfor %}
     {% for record in event.triggerRules %}
     {%- if record.isRule -%}
-    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString(false) }}
     {% elif record.instanceOf('Species') and not record.isAmount -%}
     {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
     {% endif -%}
     {% endfor %}
 
-    return {{ event.switcher.trigger.translateSymbol(img.pTranslator).toJuliaString() if event.switcher.trigger is defined else 'false' }}
+    return {{ event.switcher.trigger.translateSymbol(img.pTranslator).toJuliaString(false) if event.switcher.trigger is defined else 'false' }}
 end
 {%- endfor %}
 
@@ -313,7 +313,7 @@ function {{ id }}_{{ event.switcher.id }}_affect_func_(__integrator__)
     {%- endfor %}
     {% for record in event.affectRules %}
     {%- if record.isRule -%}
-    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString() }}
+    {{ record.id }} = {{ record.assignments.ode_.translateSymbol(img.pTranslator).toJuliaString(false) }}
     {% elif record.instanceOf('Species') and not record.isAmount -%}
     {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
     {% endif -%}
@@ -325,7 +325,7 @@ function {{ id }}_{{ event.switcher.id }}_affect_func_(__integrator__)
     {%- endfor -%}
     ) = (
     {%- for assignment in event.affect -%}
-    {{ assignment.getAssignment(event.switcher.id).translateSymbol(img.pTranslator).toJuliaString() }}, 
+    {{ assignment.getAssignment(event.switcher.id).translateSymbol(img.pTranslator).toJuliaString(false) }}, 
     {%- endfor -%}
     )
 

diff --git a/src/templates/matlab-model.m.njk b/src/templates/matlab-model.m.njk
@@ -28,7 +28,7 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
 
     {%- for functionDefinition in functionDefArray %}
     function out = {{ functionDefinition.id }}({{ functionDefinition.arguments.join(', ') }})
-        out = {{ functionDefinition.math.toMatlabString() }}
+        out = {{ functionDefinition.math.toMatlabString(false) }}
     end
     {%- endfor %}
 
@@ -55,9 +55,9 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
         {%- endfor %}
         {% for record in initRecords %}
         {% if record.getAssignment('start_') is defined -%}
-        {{ record.id }} = {{ record.getAssignment('start_').translateSymbol(pTranslator).toMatlabString() }}; % {{ record.id }}, {{ record.title }} ({{ record.units }})
+        {{ record.id }} = {{ record.getAssignment('start_').translateSymbol(pTranslator).toMatlabString(false) }}; % {{ record.id }}, {{ record.title }} ({{ record.units }})
         {%- else -%}
-        {{ record.id }} = {{ record.getAssignment('ode_').translateSymbol(pTranslator).toMatlabString() }}; % {{ record.id }}, {{ record.title }} ({{ record.units }})
+        {{ record.id }} = {{ record.getAssignment('ode_').translateSymbol(pTranslator).toMatlabString(false) }}; % {{ record.id }}, {{ record.title }} ({{ record.units }})
         {%- endif -%}
         {%- endfor %}
 
@@ -119,7 +119,7 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
         {%- for record in sharedRecords %}
         % {{ record.title }} ({{ record.units }}) {{ record.notes }}
         {% if record.isRule -%}
-        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString() }};
+        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString(false) }};
         {%- elif record.instanceOf('Species') and not record.isAmount -%}
         {{ record.id }} = {{ yTranslator[record.id] }} / {{ record.compartment }};
         {%- else -%}
@@ -168,15 +168,15 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
         {%- for record in sharedRecords %}
         % {{ record.title }} ({{ record.units }}) {{ record.notes }}
         {% if record.isRule -%}
-        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString() }};
+        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString(false) }};
         {%- elif record.instanceOf('Species') and not record.isAmount -%}
         {{ record.id }} = {{ yTranslator[record.id] }} / {{ record.compartment }};
         {%- else -%}
         {{ record.id }} = {{ yTranslator[record.id] }};
         {%- endif -%}
         {%- endfor %}
 
-        {% set trigger = event.switcher.trigger.translateSymbol(pTranslator).toMatlabString() if event.switcher.trigger is defined else 'false' -%}
+        {% set trigger = event.switcher.trigger.translateSymbol(pTranslator).toMatlabString(false) if event.switcher.trigger is defined else 'false' -%}
         if ({{ trigger }}) {#  && {{ pTranslator[event.switcher.id + '_'] }} #}
             res = 1;
         else 
@@ -196,15 +196,15 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
         {%- for record in sharedRecords %}
         % {{ record.title }} ({{ record.units }}) {{ record.notes }}
         {% if record.isRule -%}
-        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString() }};
+        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString(false) }};
         {%- elif record.instanceOf('Species') and not record.isAmount -%}
         {{ record.id }} = {{ yTranslator[record.id] }} / {{ record.compartment }};
         {%- else -%}
         {{ record.id }} = {{ yTranslator[record.id] }};
         {%- endif -%}
         {%- endfor %}
 
-        res = {{ event.switcher.trigger.translateSymbol(pTranslator).toMatlabString() if event.switcher.trigger is defined else '-1' }};
+        res = {{ event.switcher.trigger.translateSymbol(pTranslator).toMatlabString(false) if event.switcher.trigger is defined else '-1' }};
     end
     {%- endfor %}
 
@@ -219,7 +219,7 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
         {%- for record in sharedRecords %}
         % {{ record.title }} ({{ record.units }}) {{ record.notes }}
         {% if record.isRule -%}
-        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString() }};
+        {{ record.id }} = {{ record.assignments.ode_.translateSymbol(pTranslator).toMatlabString(false) }};
         {%- elif record.instanceOf('Species') and not record.isAmount -%}
         {{ record.id }} = {{ yTranslator[record.id] }} / {{ record.compartment }};
         {%- else -%}
@@ -239,9 +239,9 @@ function [ode_func, out_func, y0_, events_conditions, events_affects] = {{ names
         %%% recalculated values
         {%- for assignment in event.affect %}
         {% if assignment.instanceOf('Species') and not assignment.isAmount and not assignment.isRule -%}
-        {{ idOrSynonim(assignment) }} = ({{ assignment.getAssignment(event.switcher.id).translateSymbol(pTranslator).toMatlabString() }}) * {{ assignment.compartment }};
+        {{ idOrSynonim(assignment) }} = ({{ assignment.getAssignment(event.switcher.id).translateSymbol(pTranslator).toMatlabString(false) }}) * {{ assignment.compartment }};
         {%- else -%}
-        {{ idOrSynonim(assignment) }} = {{ assignment.getAssignment(event.switcher.id).translateSymbol(pTranslator).toMatlabString() }};
+        {{ idOrSynonim(assignment) }} = {{ assignment.getAssignment(event.switcher.id).translateSymbol(pTranslator).toMatlabString(false) }};
         {%- endif -%}
         {%- endfor %}