Merge pull request #1049 from StochSS/develop

Release v.2.1.5

client/modals.js

@@ -248,29 +248,6 @@ module.exports = {
 
       return templates.select(modalID, selectID, title, label, options)
     },
-    addExistingWorkflowToProjectHtml : (options) => {
-      let modalID = "newProjectWorkflowModal"
-      let selectID = "workflowPathInput"
-      let title = "Add Existing Workflow to Workflow Group"
-      let label = "Path to the workflow"
-      options = options.map(function (name) {
-        return `<option value="${name}">${name}</option>`
-      })
-      options = options.join(" ")
-
-      return templates.select(modalID, selectID, title, label, options)
-    },
-    addExistingWorkflowToProjectSuccessHtml : (message) => {
-      let modalID = "newProjectModelSuccessModal"
-      let title = "Success!"
-
-      return templates.message(modalID, title, message)
-    },
-    addExistingWorkflowToProjectErrorHtml : (title, message) => {
-      let modalID = "newProjectModelErrorModal"
-
-      return templates.message(modalID, title, message)
-    },
     newProjectModelSuccessHtml : (message) => {
       let modalID = "newProjectModelSuccessModal"
       let title = "Success!"
@@ -432,23 +409,23 @@ module.exports = {
     renderDefaultModeModalHtml : () => {
         let concentrationDesciption = `Variables will only be represented using continuous (floating point) values.`;
         let populationDescription = `Population - Variables will only be represented using discrete (integer count) values.`;
-        let hybridDescription = `Allows a species to be represented using continuous and/or discrete values.`;
+        let hybridDescription = `Allows a variable to be represented using continuous and/or discrete values.`;
 
         return `
             <div id="defaultModeModal" class="modal" tabindex="-1" role="dialog">
               <div class="modal-dialog" role="document">
                 <div class="modal-content info">
                   <div class="modal-header">
-                    <h5 class="modal-title">Default Variables Mode (required)</h5>
+                    <h5 class="modal-title">Default Variable Mode (required)</h5>
                     <button type="button" class="close close-modal" data-dismiss="modal" aria-label="Close">
                       <span aria-hidden="true">&times;</span>
                     </button>
                   </div>
                   <div class="modal-body">
                     <div>
                       <p>
-                        The default mode is used to set the mode of all species added to the model.  
-                        The mode of a species is used to determine how it will be represented in a Hybrid Concentration/Population simulation.
+                        The default mode is used to set the mode of all variables added to the model.  
+                        The mode of a variable is used to determine how it will be represented in a simulation.
                       </p>
                       <p>Select one of the following: </p>
                     </div>

client/models/event-assignment.js

@@ -27,4 +27,8 @@ module.exports = State.extend({
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments);
   },
+  validateComponent: function() {
+    if(!this.expression.trim()) return false;
+    return true;
+  }
 });

client/models/event-assignments.js

@@ -41,4 +41,11 @@ module.exports = Collection.extend({
   removeEventAssignment: function (eventAssignment) {
     this.remove(eventAssignment);
   },
+  validateCollection: function () {
+    if(this.length <= 0) return false;
+    for(var i = 0; i < this.length; i++) {
+      if(!this.models[i].validateComponent()) return false;
+    }
+    return true;
+  }
 });

client/models/event.js

@@ -41,8 +41,25 @@ module.exports = State.extend({
       type: 'boolean',
       default: true,
     },
+    advanced_error: 'boolean'
   },
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments);
+    this.eventAssignments.on('add change remove', this.updateValid, this)
+    this.validateComponent()
   },
+  validateComponent: function () {
+    advanced_error = false;
+    if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if(!this.triggerExpression.trim()) return false;
+    if(!this.priority.trim()) {
+      this.advanced_error = true;
+      return false;
+    };
+    if(!this.eventAssignments.validateCollection()) return false;
+    return true;
+  },
+  updateValid: function () {
+    this.collection.parent.updateValid();
+  }
 });

client/models/events.js

@@ -56,4 +56,13 @@ module.exports = Collection.extend({
     this.remove(event);
     this.parent.updateValid()
   },
+  validateCollection: function () {
+    for(var i = 0; i < this.length; i++) {
+      if(!this.models[i].validateComponent()) {
+        this.parent.error = {'id':this.models[i].compID,'type':'event'}
+        return false
+      }
+    }
+    return true;
+  }
 });

client/models/model-settings.js

@@ -21,15 +21,15 @@ var State = require('ampersand-state');
 
 module.exports = State.extend({
   props: {
-    endSim: 'number',
-    timeStep: 'number'
+    endSim: 'any',
+    timeStep: 'any'
   },
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments)
   },
   validate: function () {
-    if(this.endSim == 0 || isNaN(this.endSim)) return false;
-    if(this.timeStep == 0 || isNaN(this.timeStep)) return false;
+    if(this.endSim === "" || isNaN(this.endSim)) return false;
+    if(this.timeStep === "" || isNaN(this.timeStep)) return false;
     return true;
   }
 });

client/models/model.js

@@ -41,7 +41,7 @@ module.exports = Model.extend({
     defaultID: 'number',
     defaultMode: 'string',
     annotation: 'string',
-    volume: 'number'
+    volume: 'any'
   },
   collections: {
     species: Species,
@@ -62,19 +62,39 @@ module.exports = Model.extend({
     directory: 'string',
     isPreview: 'boolean',
     for: 'string',
-    valid: 'boolean'
+    valid: 'boolean',
+    error: 'object'
   },
   initialize: function (attrs, options){
     Model.prototype.initialize.apply(this, arguments);
+    this.species.on('add change remove', this.updateValid, this);
+    this.parameters.on('add change remove', this.updateValid, this);
+    this.reactions.on('add change remove', this.updateValid, this);
+    this.eventsCollection.on('add change remove', this.updateValid, this);
+    this.rules.on('add change remove', this.updateValid, this);
   },
   validateModel: function () {
-    if(this.volume == 0 || isNaN(this.volume)) return false;
-    if(this.species.length <= 0) return false;
-    if(this.reactions.length <= 0 && this.eventsCollection.length <= 0 && this.rules.length <= 0) return false
-    if(this.modelSettings.validate() === false) return false;
+    if(!this.species.validateCollection()) return false;
+    if(!this.parameters.validateCollection()) return false;
+    if(!this.reactions.validateCollection()) return false;
+    if(!this.eventsCollection.validateCollection()) return false;
+    if(!this.rules.validateCollection()) return false;
+    if(this.reactions.length <= 0 && this.eventsCollection.length <= 0 && this.rules.length <= 0) {
+      this.error = {"type":"process"}
+      return false;
+    }
+    if(!this.volume === "" || isNaN(this.volume)) {
+      this.error = {"type":"volume"}
+      return false
+    };
+    if(this.modelSettings.validate() === false) {
+      this.error = {"type":"timespan"}
+      return false
+    };
     return true;
   },
   updateValid: function () {
+    this.error = {}
     this.valid = this.validateModel()
   },
   getDefaultID: function () {

client/models/parameter.js

@@ -36,4 +36,9 @@ module.exports = State.extend({
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments);
   },
+  validateComponent: function () {
+    if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if(this.expression === "" || isNaN(this.expression)) return false
+    return true;
+  }
 });

client/models/parameters.js

@@ -47,4 +47,13 @@ module.exports = Collection.extend({
   removeParameter: function (parameter) {
     this.remove(parameter);
   },
+  validateCollection: function () {
+    for(var i = 0; i < this.length; i++) {
+      if(!this.models[i].validateComponent()) {
+        this.parent.error = {'id':this.models[i].compID,'type':'parameter'}
+        return false
+      }
+    }
+    return true;
+  }
 });

client/models/reaction.js

@@ -54,6 +54,13 @@ module.exports = State.extend({
   initialize: function (attrs, options) {
     var self = this;
     State.prototype.initialize.apply(this, arguments);
+    if(!this.reactionType.startsWith('custom')) {
+      let reactionType = this.updateReactionType();
+      if(this.reactionType !== reactionType){
+        this.reactionType = reactionType
+        this.buildSummary()
+      }
+    }
     this.on('change-reaction', function () {
       self.buildSummary();
       self.checkModes();
@@ -129,4 +136,39 @@ module.exports = State.extend({
     }
     this.hasConflict = Boolean(hasContinuous && (hasDynamic || hasDiscrete))
   },
+  updateReactionType: function () {
+    let numReactants = this.reactants.length
+    let numProducts = this.products.length
+    let prodRatio1 = numProducts > 0 ? this.products.models[0].ratio : 0
+    if(numReactants == 0 && numProducts == 1 && prodRatio1 == 1) return "creation";
+
+    let reactRatio1 = numReactants > 0 ? this.reactants.models[0].ratio : 0
+    let prodRatio2 = numProducts > 1 ? this.products.models[1].ratio : 0
+    if(numReactants == 1){
+      if(reactRatio1 == 1) {
+        if(numProducts == 0) return "destruction";
+        if(numProducts == 2 && prodRatio1 == 1 && prodRatio2 == 1) return "split";
+      }
+
+      if(numProducts == 1 && prodRatio1 == 1){
+        if(reactRatio1 == 1) return "change";
+        if(reactRatio1 == 2) return "dimerization";
+      }
+    }
+
+    let reactRatio2 = numReactants > 1 ? this.reactants.models[1].ratio : 0
+    if(numReactants == 2 && reactRatio1 == 1 && reactRatio2 == 1){
+      if(numProducts == 1 && prodRatio1 == 1) return "merge";
+      if(numProducts == 2 && prodRatio1 == 1 && prodRatio2 == 1) return "four";
+    }
+    return "custom-massaction"
+  },
+  validateComponent: function () {
+    if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if(!this.propensity.trim() && this.reactionType === "custom-propensity") return false;
+    if(this.reactionType.startsWith('custom')) {
+      if(this.reactants.length <= 0 && this.products.length <= 0) return false;
+    }
+    return true;
+  }
 });

client/models/reactions.js

@@ -79,6 +79,15 @@ Reactions = Collection.extend({
     this.remove(reaction);
     this.parent.updateValid()
   },
+  validateCollection: function () {
+    for(var i = 0; i < this.length; i++) {
+      if(!this.models[i].validateComponent()) {
+        this.parent.error = {'id':this.models[i].compID,'type':'reaction'}
+        return false
+      }
+    }
+    return true
+  }
 });
 
 Events.createEmitter(Reactions);

client/models/rule.js

@@ -31,4 +31,9 @@ module.exports = State.extend({
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments);
   },
+  validateComponent: function () {
+    if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if(!this.expression.trim()) return false;
+    return true;
+  }
 });

client/models/rules.js

@@ -61,4 +61,13 @@ module.exports = Collection.extend({
       return this.parent.parameters.at(0)
     }
   },
+  validateCollection: function () {
+    for(var i = 0; i < this.length; i++) {
+      if(!this.models[i].validateComponent()) {
+        this.parent.error = {'id':this.models[i].compID,'type':'rule'}
+        return false
+      }
+    }
+    return true;
+  }
 });

client/models/specie.js

@@ -24,10 +24,10 @@ module.exports = State.extend({
   props: {
     compID: 'number',
     name: 'string',
-    value: 'number',
+    value: 'any',
     mode: 'string',
-    switchTol: 'number',
-    switchMin: 'number',
+    switchTol: 'any',
+    switchMin: 'any',
     isSwitchTol: 'boolean',
     annotation: 'string',
     diffusionCoeff: 'number',
@@ -42,4 +42,13 @@ module.exports = State.extend({
   initialize: function (attrs, options) {
     State.prototype.initialize.apply(this, arguments);
   },
+  validateComponent: function () {
+    if(!this.name.trim() || this.name.match(/^\d/)) return false;
+    if(this.value === "" || isNaN(this.value)) return false;
+    if(this.mode === "dynamic") {
+      if(this.isSwitchTol && (this.switchTol === "" || isNaN(this.switchTol))) return false;
+      if(!this.isSwitchTol && (this.switchMin === "" || isNaN(this.switchMin))) return false;
+    }
+    return true;
+  }
 });

client/models/species.js

@@ -55,4 +55,17 @@ module.exports = Collection.extend({
     this.remove(specie);
     this.parent.updateValid()
   },
+  validateCollection: function () {
+    if(this.length <= 0) {
+      this.parent.error = {'type':'species'}
+      return false;
+    }
+    for(var i = 0; i < this.length; i++) {
+      if(!this.models[i].validateComponent()) {
+        this.parent.error = {'id':this.models[i].compID,'type':'species'}
+        return false
+      }
+    }
+    return true;
+  }
 });