make Component as extended Top

package.json

@@ -4,7 +4,7 @@
   "description": "Programming platform for Quantitative Systems Pharmacology modeling in NodeJS",
   "main": "src/index.js",
   "scripts": {
-    "test:dev": "mocha test/cases/14 --config=./test/.mocharc.json",
+    "test:dev": "mocha test/time-switcher/bind-error --config=./test/.mocharc.json",
     "test": "mocha test --config=./test/.mocharc.json",
     "jsdoc": "jsdoc -r -c .jsdoc.json --readme api-references.md -d docs/dev src",
     "test:cov": "nyc --reporter=lcov npm run test",

src/another-xlsx-export/_size.js

@@ -2,10 +2,10 @@ const { _Size } = require('../core/_size');
 const legalUnits = require('./legal-units');
 
 // old version
-let _toQ = _Size.prototype.toQ;
+let oldToQ = _Size.prototype.toQ;
 // new version
 _Size.prototype.toQ = function(options = {}){
-  let res = _toQ.call(this, options);
+  let res = oldToQ.call(this, options);
 
   // unit with transformation to simbio standard
   // if (options.useAnotherUnits) res.units2 = this.units;

src/container/actions.js

@@ -58,7 +58,7 @@ Container.prototype.export = function(q = {}, isCore = false) {
  */
 Container.prototype.defineUnit = function(q = {}, isCore = false){
   // normal flow
-  let unitDefInstance = new this.classes.UnitDef(q, isCore);
+  let unitDefInstance = new this.classes.UnitDef(isCore).merge(q);
   if (!unitDefInstance.errored) this.unitDefStorage.set(unitDefInstance.id, unitDefInstance);
 
   return unitDefInstance;
@@ -74,7 +74,7 @@ Container.prototype.defineUnit = function(q = {}, isCore = false){
  */
 Container.prototype.defineFunction = function(q = {}, isCore = false){
   // normal flow
-  let functionDefInstance = new this.classes.FunctionDef(q, isCore);
+  let functionDefInstance = new this.classes.FunctionDef(isCore).merge(q);
   if (!functionDefInstance.errored) this.functionDefStorage.set(functionDefInstance.id, functionDefInstance);
 
   return functionDefInstance;
@@ -90,7 +90,7 @@ Container.prototype.defineFunction = function(q = {}, isCore = false){
  */
 Container.prototype.setScenario = function(q = {}, isCore = false){
   // normal flow
-  let scenarioInstance = new this.classes.Scenario(q, isCore);
+  let scenarioInstance = new this.classes.Scenario(isCore).merge(q);
   if (!scenarioInstance.errored) this.scenarioStorage.set(scenarioInstance.id, scenarioInstance);
 
   return scenarioInstance;
@@ -159,7 +159,7 @@ Container.prototype.forceInsert = function(q = {}, isCore = false){
   }
 
   // check if class is in the list
-  let selectedClass = this._componentClasses[q.class];
+  let selectedClass = this.classes[q.class];
   if (selectedClass === undefined){
     this.logger.error(
       `"${ind}" Unknown class "${q.class}" for the component.`,
@@ -179,10 +179,8 @@ Container.prototype.forceInsert = function(q = {}, isCore = false){
   }
 
   // normal flow
-  let component = new selectedClass(isCore);
-  component._id = q.id;
+  let component = new selectedClass(isCore).merge(q);
   component.namespace = namespace; // set parent space directly to component
-  component.merge(q);
   namespace.set(q.id, component);
   return component;
 };
@@ -435,8 +433,7 @@ Container.prototype.importNS = function(_q = {}){
       || [q.prefix, component.id, q.suffix].join(''); // prefix-id-suffix as default value
 
     // cloning and update references
-    let clone = component.clone();
-    clone._id = newId;
+    let clone = component.clone().merge({id: newId});
     clone.namespace = namespace;
     clone.updateReferences(q);
 
@@ -536,8 +533,7 @@ Container.prototype.import = function(_q = {}){
   }
 
   // normal flow
-  let clone = component.clone();
-  clone._id = q.id;
+  let clone = component.clone().merge({id: q.id});
   clone.namespace = namespace;
   clone.updateReferences(q);
   namespace.set(q.id, clone);

src/container/main.js

@@ -32,7 +32,7 @@ const TopoSort = require('@insysbio/topo-sort');
  * 
  * @property {object} classes Map-like storage for all element constructors that can be created inside platform.
  *    For example the element of the type `UnitsDef` can be created as follows:
- *    ```let new_unit = new c.classes.UnitDef({id: 'new', units: 'g/litre'})```
+ *    ```let new_unit = new c.classes.UnitDef().merge({id: 'new', units: 'g/litre'})```
  *    The `new_unit` element will be automatically bound to the container and pushed to `unitDefStorage`.
  * @property {Logger} logger object providing transport of errors, warnings and info messages on Heta platform level.
  * @property {object[]} defaultLogs Default storage of errors which will be used for diagnostics.
@@ -43,7 +43,6 @@ const TopoSort = require('@insysbio/topo-sort');
  * @property {Map<string,Namespace>} namespaceStorage Storage for `Namespace` instances. Key is a string identifier.
  *    There is a default namespace with identifier `nameless` which will be used as a default namespace 
  *    for all components where namespace name is not set.
- * @property {object} _componentClasses map-like structure for storing all available constructors for `Component`s.
  * @property {object} _builder reference to the parent builder object (if exists).
  */
 class Container {
@@ -60,6 +59,35 @@ class Container {
     this.classes.FunctionDef.prototype._container = this;
     this.classes.Scenario = class extends Scenario {};
     this.classes.Scenario.prototype._container = this;
+    //
+    this.classes.Component = class extends Component {};
+    this.classes.Component.prototype._container = this;
+    this.classes.Record = class extends Record {};
+    this.classes.Record.prototype._container = this;
+    this.classes.Compartment = class extends Compartment {};
+    this.classes.Compartment.prototype._container = this;
+    this.classes.Species = class extends Species {};
+    this.classes.Species.prototype._container = this;
+    this.classes.Reaction = class extends Reaction {};
+    this.classes.Reaction.prototype._container = this;
+    this.classes.Process = class extends Process {};
+    this.classes.Process.prototype._container = this;
+    this.classes.DSwitcher = class extends DSwitcher {};
+    this.classes.DSwitcher.prototype._container = this;
+    this.classes.StopSwitcher = class extends StopSwitcher {};
+    this.classes.StopSwitcher.prototype._container = this;
+    this.classes.CSwitcher = class extends CSwitcher {};
+    this.classes.CSwitcher.prototype._container = this;
+    this.classes.TimeSwitcher = class extends TimeSwitcher {};
+    this.classes.TimeSwitcher.prototype._container = this;
+    this.classes.ReferenceDefinition = class extends ReferenceDefinition {};
+    this.classes.ReferenceDefinition.prototype._container = this;
+    this.classes.Page = class extends Page {};
+    this.classes.Page.prototype._container = this;
+    this.classes.Const = class extends Const {};
+    this.classes.Const.prototype._container = this;
+    this.classes.TimeScale = class extends TimeScale {};
+    this.classes.TimeScale.prototype._container = this;  
 
     // logger
     this.logger = new Logger();
@@ -322,21 +350,4 @@ class Container {
 
 // only component classes are stored
 
-Container.prototype._componentClasses = {
-  Component,
-  Record,
-  Compartment,
-  Species,
-  Process,
-  Reaction,
-  DSwitcher,
-  StopSwitcher,
-  CSwitcher,
-  TimeSwitcher,
-  ReferenceDefinition,
-  Page,
-  Const,
-  TimeScale
-};
-
 module.exports = Container;

src/core/_size.js

@@ -1,5 +1,43 @@
 const { Component } = require('./component');
 const { Unit } = require('./unit');
+const { ajv } = require('../utils');
+
+const schema = {
+  type: "object",
+  properties: {
+    units: { anyOf: [
+       { type: 'number', enum: [1] },
+       { $ref: '#/definitions/UnitsExpr' },
+       { type: 'array', items: { '$ref': '#/definitions/UnitComponent' } },
+       { type: 'null' }
+    ] }
+  },
+  definitions:{
+    UnitsExpr: {
+       description: 'Unit expression, see qsp-units project.',
+       type: 'string',
+       pattern: '^[_a-zA-Z0-9./*^ ()+-]+$',
+       example: "1/h * ms"
+     },
+    UnitComponent: {
+      type: 'object',
+      required: ['kind'],
+      properties: {
+        kind: { '$ref': '#/definitions/ID' },
+        multiplier: { type: 'number', exclusiveMinimum: 0 },
+        exponent: { type: 'number' }
+      },
+      example: { kind: 'mole', multiplier: 1e-6, exponent: 1 }
+    },
+    ID: {
+       description: 'First character is letter, others are letter, digit or lodash.',
+       type: 'string',
+       minLength: 1,
+       pattern: '^[_a-zA-Z][_a-zA-Z0-9]*$',
+       example: 'x_12_'
+     }
+  }
+};
 
 /*
   Abstract class _Size
@@ -17,7 +55,7 @@ const { Unit } = require('./unit');
 class _Size extends Component {
   merge(q = {}){
     super.merge(q);
-    let logger = this.namespace?.container?.logger;
+    let logger = this._container?.logger;
     let valid = _Size.isValid(q, logger);
     if (valid) {
       if (q.units !== undefined) {
@@ -60,8 +98,8 @@ class _Size extends Component {
   /** Additional check of units items */
   bind(namespace){
     super.bind(namespace);
-    let logger = this.namespace.container.logger;
-    let storage = this.namespace.container.unitDefStorage;
+    let logger = this._container?.logger;
+    let storage = this._container?.unitDefStorage;
 
     if (this.unitsParsed) {
       this.unitsParsed.forEach((x) => {
@@ -95,7 +133,7 @@ class _Size extends Component {
           .rebase(legalUnits)
           .toString(usePefix);
       } catch(err) {
-        let logger = this.namespace.container.logger;
+        let logger = this._container?.logger;
         let msg = err.message;
         logger.warn(msg);
         return undefined;
@@ -104,8 +142,12 @@ class _Size extends Component {
       return undefined;
     }
   }
+  static get validate() {
+    return ajv.compile(schema);
+  }
   toQ(options = {}){
     let res = super.toQ(options);
+
     if (this.unitsParsed) {
       if (options.noUnitsExpr) {
         res.units = this.unitsParsed.toQ(options);
@@ -116,14 +158,8 @@ class _Size extends Component {
 
     return res;
   }
-  _references(){
-    let classSpecificRefs = [];
-
-    return super._references()
-      .concat(classSpecificRefs);
-  }
 }
 
 module.exports = {
   _Size
-};
+};

src/core/_switcher.js

@@ -1,4 +1,27 @@
 const { Component } = require('./component');
+const { ajv } = require('../utils');
+
+const schema = {
+  type: 'object',
+  properties: {
+    atStart: {oneOf: [
+      {
+        description: 'If true than the condition will be checked at start_',
+        enum: [true, false, 1, 0],
+        default: false
+      },
+      { type: 'null' }
+    ]},
+    active: {oneOf: [
+      {
+        description: 'if false the event will not run.',
+        enum: [true, false, 1, 0],
+        default: true
+      },
+      { type: 'null' }
+    ]}
+  }
+};
 
 /*
   _Switcher abstract class
@@ -14,7 +37,7 @@ class _Switcher extends Component {
   }
   merge(q = {}){
     super.merge(q);
-    let logger = this.namespace?.container?.logger;
+    let logger = this._container?.logger;
     let valid = _Switcher.isValid(q, logger);
 
     if (valid) {
@@ -51,6 +74,9 @@ class _Switcher extends Component {
 
     return res;
   }
+  static get validate() {
+    return ajv.compile(schema);
+  }
 }
 
 _Switcher._requirements = {

src/core/c-switcher.js

@@ -1,5 +1,24 @@
 const { _Switcher } = require('./_switcher');
 const { Expression } = require('./expression');
+const { ajv } = require('../utils');
+
+const schema = {
+  type: "object",
+  properties: {
+    trigger: {oneOf: [
+      { '$ref': '#/definitions/ExprString' },
+      { type: "null" }
+    ]}
+  },
+  definitions: {
+    ExprString: {
+      description: 'Expression as string. Currently pattern does not analyze expressions.',
+      type: 'string',
+      minLength: 1,
+      pattern: '[a-zA-Z0-9. -+/*^()]*$'
+    }
+  }
+};
 
 /*
   CSwitcher class
@@ -11,7 +30,7 @@ const { Expression } = require('./expression');
 class CSwitcher extends _Switcher {
   merge(q = {}){
     super.merge(q);
-    let logger = this.namespace?.container?.logger;
+    let logger = this._container?.logger;
     let valid = CSwitcher.isValid(q, logger);
 
     if (valid) {
@@ -60,7 +79,7 @@ class CSwitcher extends _Switcher {
   }
   bind(namespace){
     super.bind(namespace);
-    let {logger, functionDefStorage} = this.namespace.container;
+    let {logger, functionDefStorage} = this._container;
 
     // get list of 
     this.trigger && this.trigger.dependOnNodes().forEach((node) => {
@@ -105,7 +124,7 @@ class CSwitcher extends _Switcher {
   Works only for bound switchers
   */
   checkUnits(){
-    let logger = this.namespace.container.logger;
+    let logger = this._container?.logger;
 
     if (typeof this.trigger !== 'undefined') { // skip empty
       let rightSideUnit = this.trigger.calcUnit(this);
@@ -114,6 +133,9 @@ class CSwitcher extends _Switcher {
       }
     }
   }
+  static get validate() {
+    return ajv.compile(schema);
+  }
 }
 
 CSwitcher._requirements = {