remove _logger from Expression

src/core/c-switcher.js

@@ -18,7 +18,6 @@ class CSwitcher extends _Switcher {
       if (typeof q.trigger !== 'undefined') {
         try { // this is for the cases of wrong ExprString structure
           let expr = Expression.fromString(q.trigger);
-          expr._logger = logger;
           if (!expr.hasBooleanResult()) {
             this.trigger = expr;
           } else {

src/core/d-switcher.js

@@ -21,7 +21,6 @@ class DSwitcher extends _Switcher {
         q.trigger += '';
         try { // this is for the cases of wrong ExprString structure
           let expr = Expression.fromString(q.trigger);
-          expr._logger = logger;
           if (expr.hasBooleanResult()) {
             this.trigger = expr; 
           } else {

src/core/expression.js

@@ -10,10 +10,6 @@ const { uniqBy } = require('../utils');
 class Expression {
   /*
     exprParsed: <mathjs.Node>
-
-    XXX: currently Expression instances have _logger property
-    which is set after expression creation
-    in future versions it should be resolved by automatic addition of __platform__ property 
   */
   constructor(exprParsed){ 
     this.exprParsed = exprParsed;
@@ -68,7 +64,6 @@ class Expression {
   clone(){
     let clonedMath = this.exprParsed.cloneDeep();
     let expr = new Expression(clonedMath);
-    expr._logger = this._logger;
     return expr;
   }
   // substitute user defined functions by their content, return Expression 
@@ -82,7 +77,6 @@ class Expression {
     });
 
     let expr = new Expression(transformed);
-    expr._logger = this._logger;
 
     return expr;
   }
@@ -157,7 +151,6 @@ class Expression {
     ]);
 
     let expr = new Expression(node);
-    expr._logger = this._logger; // set the same logger
 
     return expr;
   }

src/core/function-def.js

@@ -60,7 +60,6 @@ class FunctionDef extends Top {
     if (q.math) {
       try {
         var expr = Expression.fromString(q.math);
-        expr._logger = logger;
         if (!expr.hasBooleanResult()) {
           this.math = expr;
         } else {

src/core/record.js

@@ -26,7 +26,6 @@ class Record extends _Size {
           if (typeof x === 'string' || typeof x === 'number') {
             try { // this is for the cases of wrong ExprString structure
               let expr = Expression.fromString(x);
-              expr._logger = logger;
               if (!expr.hasBooleanResult()) {
                 this.assignments[key] = expr;
               } else {

src/core/stop-switcher.js

@@ -21,7 +21,6 @@ class StopSwitcher extends _Switcher {
         q.trigger += '';
         try { // this is for the cases of wrong ExprString structure
           let expr = Expression.fromString(q.trigger);
-          expr._logger = logger;
           if (expr.hasBooleanResult()) {
             this.trigger = expr; 
           } else {

src/dbsolve-export/expression.js

@@ -1,6 +1,6 @@
 const { Expression } = require('../core/expression');
 
-Expression.prototype.toSLVString = function(powTransform = 'keep', substituteByDefinitions = true) {
+Expression.prototype.toSLVString = function(logger, powTransform = 'keep', substituteByDefinitions = true) {
   let tree = substituteByDefinitions ? this.substituteByDefinitions().exprParsed : this.exprParsed;
 
   if (['keep', 'operator', 'function'].indexOf(powTransform) === -1) {
@@ -140,7 +140,7 @@ Expression.prototype.toSLVString = function(powTransform = 'keep', substituteByD
     }
     if (node.type === 'FunctionNode' && node.fn.name === 'piecewise') {
       let msg = `DBS and SLV formats do not support "piecewise" function, got "${node.toString()}"`;
-      this._logger.error(msg);
+      logger && logger.error(msg);
       let args = node.args
         .map((arg) => arg.toString(options));
       return `piecewise(${args.join(',')})`;
@@ -173,7 +173,7 @@ Expression.prototype.toSLVString = function(powTransform = 'keep', substituteByD
         return `ifgt(0, 1, ${trueExpr}, ${falseExpr})`;
       } else if (condition.type === 'OperatorNode') {
         let msg = `SLV format does not support boolean operators, got "${node.toString()}"`;
-        this._logger.error(msg);
+        logger && logger.error(msg);
         return `ifgt([error], [error], ${trueExpr}, ${falseExpr})`;
       }
     }

src/dbsolve-export/index.js

@@ -18,7 +18,7 @@ class DBSolveExport extends AbstractExport{
     super(q, isCore);
 
     // check arguments here
-    let logger = this._container.logger;
+    let { logger } = this._container;
     let valid = DBSolveExport.isValid(q, logger);
     if (!valid) { this.errored = true; return; }
 
@@ -45,7 +45,7 @@ class DBSolveExport extends AbstractExport{
    * @return {string} Text code of exported format.
    */
   makeText() {
-    //let logger = this._container.logger;
+    //let { logger } = this._container;
 
     let selectedNamespaces = this.selectedNamespaces();
 

src/dbsolve-export/namespace.js

@@ -75,7 +75,7 @@ Namespace.prototype.getDBSolveImage = function(powTransform, groupConstBy, versi
             target: record.id + (record.isDynamic ? '_' : ''),
             multiply: 0,
             add: record.id + '_' + switcher.id + '_',
-            expr: expr.toSLVString(powTransform)
+            expr: expr.toSLVString(logger, powTransform)
           };
           timeEvents.push(evt);
         });
@@ -169,5 +169,6 @@ Namespace.prototype.getDBSolveImage = function(powTransform, groupConstBy, versi
     discreteEvents,
     continuousEvents,
     groupedConst,
+    logger
   };
 };

src/mrgsolve-export/expression.js

@@ -1,6 +1,6 @@
 const { Expression } = require('../core/expression');
 
-Expression.prototype.toCString = function(_mathOptions = {}, substituteByDefinitions = true){
+Expression.prototype.toCString = function(logger, _mathOptions = {}, substituteByDefinitions = true){
   // set defaults
   let mathOptions = Object.assign({
     timeVariable: 'SOLVERTIME'
@@ -36,7 +36,7 @@ Expression.prototype.toCString = function(_mathOptions = {}, substituteByDefinit
     // piecewise function
     if (node.type === 'FunctionNode' && node.fn.name === 'piecewise') {
       let msg = `mrgsolve format does not support "piecewise" function, got "${node.toString()}"`;
-      this._logger.error(msg);
+      logger && logger.error(msg);
       let args = node.args
         .map((arg) => arg.toString(options));
       return `piecewise(${args.join(',')})`;

src/mrgsolve-export/namespace.js

@@ -3,6 +3,7 @@ require('./expression');
 const { intersection } = require('../utils');
 
 Namespace.prototype.getMrgsolveImage = function() {
+  let { logger } = this.container;
   // set dynamic variables
   let dynamicRecords = this
     .selectByInstanceOf('Record')
@@ -19,7 +20,6 @@ Namespace.prototype.getMrgsolveImage = function() {
       let deps = record.dependOn('start_', true);
       let diff = intersection(dynamicIds, deps);
       if (diff.length > 0) {
-        let logger = this.container.logger;
         let errorMsg = `Mrgsolve does not support when initial assignments depends on dynamic values: ${diff}\n`
           + `${record.index} .= ${record.assignments.start_.toString()}`;
 
@@ -123,6 +123,7 @@ Namespace.prototype.getMrgsolveImage = function() {
     ruleRecords,
     timeEvents,
     continuousEvents,
-    output
+    output,
+    logger
   };
-};
+};

src/templates/dbsolve-model.slv.njk

@@ -435,9 +435,9 @@ if(t == 0){
     // initialization of Records
     {%- for record in initRecords %}
     {% if record.isRule -%}
-    {{ record.id }} = {{ record.getAssignment('ode_').toSLVString(powTransform) }};
+    {{ record.id }} = {{ record.getAssignment('ode_').toSLVString(logger, powTransform) }};
     {%- else -%}
-    {{ record.id }} = {{ record.getAssignment('start_').toSLVString(powTransform) }};
+    {{ record.id }} = {{ record.getAssignment('start_').toSLVString(logger, powTransform) }};
     {%- endif %}
     {%- endfor %}
     // calculate initial amounts
@@ -456,7 +456,7 @@ if(t == 0){
 //!! {{ record.id }}
 {%- endif %}
 {% if record.isRule -%}
-{{ record.id }} = {{ record.getAssignment('ode_').toSLVString(powTransform) }};
+{{ record.id }} = {{ record.getAssignment('ode_').toSLVString(logger, powTransform) }};
 {%- elif record.isDynamic -%}
 {{ record.id }} = ({{ record.id }}_ + {{ record.id }}_start__){{ ' / '+ record.compartment if record.instanceOf('Species') and not record.isAmount}};
 {%- endif -%}
@@ -478,20 +478,20 @@ F[{{ loop.index }}] = {{ diff(dynamic.backReferences) }};
 {%- for evt in discreteEvents %}
 if({{ evt.switcher.id }}_ > 0){
 if({{ evt.switcher.id }}_down_ == 0){
-  if({{ evt.switcher.trigger.toSLVString(powTransform) if evt.switcher.trigger is defined }}){
+  if({{ evt.switcher.trigger.toSLVString(logger, powTransform) if evt.switcher.trigger is defined }}){
     {%- for assign in evt.assignments %}
     {%- if assign.targetObj.isDynamic %}
-    {{ assign.targetObj.id }}_start__ = {{ assign.expr.toSLVString(powTransform) -}} 
+    {{ assign.targetObj.id }}_start__ = {{ assign.expr.toSLVString(logger, powTransform) -}} 
       - ({{ assign.targetObj.id }}){{ ' * '+ assign.targetObj.compartment if assign.targetObj.instanceOf('Species') and not assign.targetObj.isAmount -}}
       + {{ assign.targetObj.id }}_start__;
     {%- else %}
-    {{ assign.targetObj.id }} = {{ assign.expr.toSLVString(powTransform) }};
+    {{ assign.targetObj.id }} = {{ assign.expr.toSLVString(logger, powTransform) }};
     {%- endif %}
     {%- endfor %}
     {{ evt.switcher.id }}_down_ = 1;
   }else{}
 }else{
-  if({{ evt.switcher.trigger.toSLVString(powTransform) if evt.switcher.trigger is defined }}){}else{
+  if({{ evt.switcher.trigger.toSLVString(logger, powTransform) if evt.switcher.trigger is defined }}){}else{
     {{ evt.switcher.id }}_down_ = 0;
   }
 }
@@ -501,20 +501,20 @@ if({{ evt.switcher.id }}_down_ == 0){
 {%- for evt in continuousEvents %}
 if({{ evt.switcher.id }}_ > 0){
 if({{ evt.switcher.id }}_down_ == 0){
-  if({{ evt.switcher.trigger.toSLVString(powTransform) + '>=0' if evt.switcher.trigger is defined }}){
+  if({{ evt.switcher.trigger.toSLVString(logger, powTransform) + '>=0' if evt.switcher.trigger is defined }}){
     {%- for assign in evt.assignments %}
     {%- if assign.targetObj.isDynamic %}
-    {{ assign.targetObj.id }}_start__ = {{ assign.expr.toSLVString(powTransform) -}} 
+    {{ assign.targetObj.id }}_start__ = {{ assign.expr.toSLVString(logger, powTransform) -}} 
       - ({{ assign.targetObj.id }}){{ ' * '+ assign.targetObj.compartment if assign.targetObj.instanceOf('Species') and not assign.targetObj.isAmount -}}
       + {{ assign.targetObj.id }}_start__;
     {%- else %}
-    {{ assign.targetObj.id }} = {{ assign.expr.toSLVString(powTransform) }};
+    {{ assign.targetObj.id }} = {{ assign.expr.toSLVString(logger, powTransform) }};
     {%- endif %}
     {%- endfor %}
     {{ evt.switcher.id }}_down_ = 1;
   }else{}
 }else{
-  if({{ evt.switcher.trigger.toSLVString(powTransform) + '>=0' if evt.switcher.trigger is defined }}){}else{
+  if({{ evt.switcher.trigger.toSLVString(logger, powTransform) + '>=0' if evt.switcher.trigger is defined }}){}else{
     {{ evt.switcher.id }}_down_ = 0;
   }
 }

src/templates/mrgsolve-model.cpp.njk

@@ -42,7 +42,7 @@ $GLOBAL
 
 $PREAMBLE
 {%- for record in initRecords %}
-{{ "//" if record.isDynamic }}double {{ record.id }} = {{ record.assignments.start_.toCString() }}; 
+{{ "//" if record.isDynamic }}double {{ record.id }} = {{ record.assignments.start_.toCString(logger) }}; 
 {%- endfor %}
 {%- for evt in continuousEvents %}
 bool {{ evt.switcher.id }}_down_ = false;
@@ -53,7 +53,7 @@ self.mevent({{ evt.switcher.getStart() | default('0.0')}}, {{ loop.index0 + 10 }
 
 $MAIN
 {%- for variable in initRecords | filter2("isDynamic", true) %}
-{{  variable.id }}{{ "_amt_" if (variable.className==="Species" and not variable.isAmount) }}_0 = ({{ variable.assignments.start_.toCString() }}){% if variable.className==="Species" and not variable.isAmount %} * {{ variable.compartment }}{% endif %}; 
+{{  variable.id }}{{ "_amt_" if (variable.className==="Species" and not variable.isAmount) }}_0 = ({{ variable.assignments.start_.toCString(logger) }}){% if variable.className==="Species" and not variable.isAmount %} * {{ variable.compartment }}{% endif %}; 
 {%- endfor %}
 
 {% if continuousEvents|length + timeEvents|length > 0 -%}
@@ -65,12 +65,12 @@ if ({{ evt.switcher.id }}_ && EVID=={{ loop.index0 + 10 }}{{ ' && TIME>0.0' if n
   {%- if assign.num >= 0 %} {# for synamic #}
   {%- set evtId = 'evt_' + assign.target + '_' %}
   mrg::evdata {{ evtId }}(TIME, 8);
-  {{ evtId }}.amt = {{ assign.expr.toCString({timeVariable: 'TIME'}) }};
+  {{ evtId }}.amt = {{ assign.expr.toCString(logger, {timeVariable: 'TIME'}) }};
   {{ evtId }}.cmt = {{ assign.num + 1}};
   {{ evtId }}.now = true;
   self.mevector.push_back({{ evtId }});
   {%- else %} {# for static #}
-  {{ assign.target }} = {{ assign.expr.toCString({timeVariable: 'TIME'}) }};
+  {{ assign.target }} = {{ assign.expr.toCString(logger, {timeVariable: 'TIME'}) }};
   {%- endif %}
   {%- endfor %}
   {%- if evt.switcher.getPeriod() is defined %}
@@ -84,22 +84,22 @@ if ({{ evt.switcher.id }}_ && EVID=={{ loop.index0 + 10 }}{{ ' && TIME>0.0' if n
 {%- endfor %}
 {%- for evt in continuousEvents %}
 // {{ evt.switcher.id }} @{{ evt.switcher.className }}
-{%- set evtCondition = evt.switcher.trigger.toCString({timeVariable: 'TIME'}) + '>=0.0' 
+{%- set evtCondition = evt.switcher.trigger.toCString(logger, {timeVariable: 'TIME'}) + '>=0.0' 
   if evt.switcher.className == 'CSwitcher'
-  else evt.switcher.trigger.toCString({timeVariable: 'TIME'}) %}
+  else evt.switcher.trigger.toCString(logger, {timeVariable: 'TIME'}) %}
 if ({{ evt.switcher.id }}_ && !{{ evt.switcher.id }}_down_ && ({{ evtCondition }}){{ ' && TIME>0.0' if not evt.switcher.atStart }}) {
   {{ evt.switcher.id }}_down_ = true;
 
   {%- for assign in evt.assignments %}
   {%- if assign.num >= 0 %} {# for synamic #}
   {%- set evtId = 'evt_' + assign.target + '_' %}
   mrg::evdata {{ evtId }}(TIME, 8);
-  {{ evtId }}.amt = {{ assign.expr.toCString({timeVariable: 'TIME'}) }};
+  {{ evtId }}.amt = {{ assign.expr.toCString(logger, {timeVariable: 'TIME'}) }};
   {{ evtId }}.cmt = {{ assign.num + 1}};
   {{ evtId }}.now = true;
   self.mevector.push_back({{ evtId }});
   {%- else %} {# for static #}
-  {{ assign.target }} = {{ assign.expr.toCString({timeVariable: 'TIME'}) }};
+  {{ assign.target }} = {{ assign.expr.toCString(logger, {timeVariable: 'TIME'}) }};
   {%- endif %}
   {%- endfor %}
 } else {
@@ -115,7 +115,7 @@ double {{ ts.id }} = {{ ts.slope }} * SOLVERTIME + {{ ts.intercept }};
 {%- endfor %}
 {%- for record in ruleRecords %}
 // @{{ record.className }} '{{ record.title }}'
-{{ "double " if not record.assignments.start_ }}{{ record.id }} = {{  record.assignments.ode_.toCString({timeVariable: 'SOLVERTIME'}) }};
+{{ "double " if not record.assignments.start_ }}{{ record.id }} = {{  record.assignments.ode_.toCString(logger) }};
 {%- endfor %}
 {% for variable in dynamicRecords %}
 dxdt_{{ variable.id }}{{ "_amt_" if variable.className==="Species" and not variable.isAmount }} =

src/templates/slv-blocks-template.slv.njk

@@ -75,7 +75,7 @@ default_compartment_ = 1; // {units: UL} This is fake compartment to support com
 //
 //!! {{ rule.id }}
 {%- endif %}
-{{ rule.id }} = {{ rule.assignments.ode_.toSLVString(powTransform) }}; // @{{ rule.className }} {{ "'"+rule.title+"'" if rule.title }} {units: {{ rule.units|default('?') }}}
+{{ rule.id }} = {{ rule.assignments.ode_.toSLVString(logger, powTransform) }}; // @{{ rule.className }} {{ "'"+rule.title+"'" if rule.title }} {units: {{ rule.units|default('?') }}}
 {%- endfor %}
 //! Differential equations, count: {{ variables|length}}
 {%- for dynamic in variables %}