Variable target update

client/job-view/job-view.js

@@ -46,10 +46,10 @@ module.exports = View.extend({
   },
   render: function (attrs, options) {
   	View.prototype.render.apply(this, arguments);
-  	if(this.model.status !== "error") {
+  	if(this.model.status === "complete") {
       this.renderResultsView();
     }
-    if(!this.readOnly) {
+    if(!this.readOnly && this.model.status !== "running") {
       this.renderLogsView();
     }
     this.renderSettingsView();

client/model-view/model-view.js

@@ -106,11 +106,9 @@ module.exports = View.extend({
       });
       this.model.eventsCollection.on("add change remove", () => {
         this.updateSpeciesInUse();
-        this.updateParametersInUse();
       });
       this.model.rules.on("add change remove", () => {
         this.updateSpeciesInUse();
-        this.updateParametersInUse();
       });
     }
   },
@@ -429,14 +427,6 @@ module.exports = View.extend({
         updateInUse(reaction.rate);
       }
     });
-    events.forEach((event) => {
-      event.eventAssignments.forEach((assignment) => {
-        updateInUse(assignment.variable);
-      });
-    });
-    rules.forEach((rule) => {
-      updateInUse(rule.variable);
-    });
   },
   updateSpeciesInUse: function () {
     let species = this.model.species;
@@ -450,6 +440,10 @@ module.exports = View.extend({
           specie.inUse = true;
         });
     }
+    let updateInUseForRate = (rate) => {
+      specie = species.get(rate.compID, 'compID')
+      if(specie) { specie.inUse = true; }
+    }
     let updateInUseForOther = (specie) => {
       _.where(species.models, { compID: specie.compID })
        .forEach((specie) => {
@@ -459,6 +453,9 @@ module.exports = View.extend({
     reactions.forEach((reaction) => {
       reaction.products.forEach(updateInUseForReaction);
       reaction.reactants.forEach(updateInUseForReaction);
+      if(reaction.reactionType !== 'custom-propensity') {
+        updateInUseForRate(reaction.rate);
+      }
     });
     events.forEach((event) => {
       event.eventAssignments.forEach((assignment) => {

client/model-view/templates/editSpecie.pug

@@ -9,10 +9,16 @@ div.mx-1
 
       div.pl-2(data-hook="input-name-container")
 
-    div.col-sm-5
+    div.col-sm-3
 
       div(data-hook="input-value-container")
 
+    div.col-sm-2
+
+      div.pl-3
+
+        input(type="checkbox" data-hook="observable")
+
     div.col-sm-2
 
       div.tooltip-icon-large(data-hook="annotation-tooltip" data-html="true" data-toggle="tooltip" title=this.model.annotation || "Click 'Add' to add an annotation") <svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="file-alt" class="svg-inline--fa fa-file-alt fa-w-12" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 384 512"><path fill="currentColor" d="M224 136V0H24C10.7 0 0 10.7 0 24v464c0 13.3 10.7 24 24 24h336c13.3 0 24-10.7 24-24V160H248c-13.2 0-24-10.8-24-24zm64 236c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-64c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12v8zm0-72v8c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-8c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12zm96-114.1v6.1H256V0h6.1c6.4 0 12.5 2.5 17 7l97.9 98c4.5 4.5 7 10.6 7 16.9z"></path></svg>

client/model-view/templates/rulesView.pug

@@ -22,7 +22,7 @@ div#rules-editor.card
 
   div.card-body
     p.mb-0
-     | Equations that determine the value (assignment rule) or rates of change (rate rule) of <i>Variables</i> or <i>Parameter</i>.
+     | Equations that determine the value (assignment rule) or rates of change (rate rule) of <i>Variables</i>.
     ul.mb-0
       li A <b>'Rate Rule'</b> corresponds to a function in the form of <span data-hook="rr-doc-func"></span>
       li An <b>'Assignment Rule'</b> correspond to a function in the form of <span data-hook="ar-doc-func"></span>

client/model-view/templates/speciesView.pug

@@ -38,12 +38,18 @@ div#species-editor.card
 
             div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.name) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
-          div.col-sm-5
+          div.col-sm-3
 
             h6.inline <b>Initial Condition</b>
 
             div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.initialValue) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
 
+          div.col-sm-2
+
+            h6.inline <b>Observable</b>
+
+            div.tooltip-icon(data-html="true" data-toggle="tooltip" title=this.tooltips.observable) <sup><svg aria-hidden="true" focusable="false" data-prefix="fas" data-icon="info" class="svg-inline--fa fa-info fa-w-6" role="img" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 192 512"><path fill="currentColor" d="M20 424.229h20V279.771H20c-11.046 0-20-8.954-20-20V212c0-11.046 8.954-20 20-20h112c11.046 0 20 8.954 20 20v212.229h20c11.046 0 20 8.954 20 20V492c0 11.046-8.954 20-20 20H20c-11.046 0-20-8.954-20-20v-47.771c0-11.046 8.954-20 20-20zM96 0C56.235 0 24 32.235 24 72s32.235 72 72 72 72-32.235 72-72S135.764 0 96 0z"></path></svg></sup>
+
           div.col-sm-2
 
             h6.inline <b>Annotation</b>
@@ -80,10 +86,14 @@ div#species-editor.card
 
             h6.inline <b>Mode</b>
 
-          div.col-sm-4(data-hook="species-switching-header")
+          div.col-sm-2(data-hook="species-switching-header")
 
             h6.inline <b>Switch Tolerance/Minimum Value for Switching</b>
 
+          div.col-sm-2
+
+            h6.inline <b>Observable</b>
+
           div.col-sm-2(data-hook="species-annotation-header")
 
             h6.inline <b>Annotation</b>

client/model-view/templates/viewSpecie.pug

@@ -18,9 +18,15 @@ div.mx-1
       div=this.model.mode
 
     if this.model.mode === "dynamic"
-      div.col-sm-4
+      div.col-sm-2
         div=this.switchingValWithLabel
 
+    div.col-sm-2
+
+      div.pl-3
+
+        input(type="checkbox" data-hook="observable" checked=this.model.observable)
+
     div.col-sm-2
 
       if this.model.annotation

client/model-view/views/event-assignment-view.js

@@ -43,15 +43,9 @@ module.exports = View.extend({
   },
   getOptions: function () {
     var species = this.model.collection.parent.collection.parent.species;
-    var parameters = this.model.collection.parent.collection.parent.parameters;
-    var specs = species.map(function (specie) {
+    var options = species.map(function (specie) {
       return [specie.compID, specie.name];
     });
-    var params = parameters.map(function (parameter) {
-      return [parameter.compID, parameter.name];
-    });
-    let options = [{groupName: Boolean(specs) ? "Variables" : "Variables (empty)", options: specs},
-                   {groupName: Boolean(params) ? "Parameters" : "Parameters (empty)", options: params}];
     return options;
   },
   removeAssignment: function () {
@@ -60,22 +54,8 @@ module.exports = View.extend({
     this.collection.parent.collection.trigger('change');
   },
   selectAssignmentVariable: function (e) {
-    var species = this.model.collection.parent.collection.parent.species;
-    var parameters = this.model.collection.parent.collection.parent.parameters;
-    var val = Number(e.target.value);
-    var eventVar = species.filter(function (specie) {
-      if(specie.compID === val) {
-        return specie;
-      }
-    });
-    if(!eventVar.length) {
-      eventVar = parameters.filter(function (parameter) {
-        if(parameter.compID === val) {
-          return parameter;
-        }
-      });
-    }
-    this.model.variable = eventVar[0];
+    let species = this.model.collection.parent.collection.parent.species;
+    this.model.variable = species.get(Number(e.target.value), 'compID');
     this.updateViewer();
     this.model.collection.parent.collection.trigger('change');
   },
@@ -107,7 +87,7 @@ module.exports = View.extend({
           name: 'variable',
           required: true,
           idAttributes: 'cid',
-          groupOptions: options,
+          options: options,
           value: this.model.variable.compID
         });
       }

client/model-view/views/parameters-view.js

@@ -49,24 +49,6 @@ module.exports = View.extend({
           }
         }
       });
-      this.collection.parent.eventsCollection.map((event) => {
-        event.eventAssignments.map((assignment) => {
-          if(assignment.variable.compID === compID) {
-            assignment.variable = parameter;
-          }
-        })
-        if(event.selected) {
-          event.trigger('change-event');
-        }
-      });
-      this.collection.parent.rules.map((rule) => {
-        if(rule.variable.compID === compID) {
-          rule.variable = parameter;
-        }
-      });
-      if(this.parent.rulesView) {
-        this.parent.rulesView.renderEditRules();
-      }
     });
   },
   render: function () {

client/model-view/views/reaction-view.js

@@ -155,6 +155,19 @@ module.exports = View.extend({
       self.parent.renderEditReactionView();
     });
   },
+  getOptions: function () {
+    var species = this.model.collection.parent.species;
+    var parameters = this.model.collection.parent.parameters;
+    var specs = species.map(function (specie) {
+      return [specie.compID, specie.name];
+    });
+    var params = parameters.map(function (parameter) {
+      return [parameter.compID, parameter.name];
+    });
+    let options = [{groupName: Boolean(specs) ? "Variables" : "Variables (empty)", options: specs},
+                   {groupName: Boolean(params) ? "Parameters" : "Parameters (empty)", options: params}];
+    return options;
+  },
   getReactionTypes: function () {
     let disableTypes = this.model.collection.parent.parameters.length == 0;
     let options = _.map(ReactionTypes, function (val, key) {
@@ -289,14 +302,18 @@ module.exports = View.extend({
         viewOptions['options'] = [];
         viewOptions['unselectedText'] = "N/A";
       }else{
-        // make sure the reaction has a rate and that rate exists in the parameters collection
+        // make sure the reaction has a rate and that rate exists in the species or parameters collection
         let paramIDs = this.model.collection.parent.parameters.map(function (param) {
           return param.compID;
         });
-        if(!this.model.rate.compID || !paramIDs.includes(this.model.rate.compID)) {
+        let specIDs = this.model.collection.parent.species.map(function (spec) {
+          return spec.compID;
+        });
+        let rateExists = paramIDs.includes(this.model.rate.compID) || specIDs.includes(this.model.rate.compID);
+        if(!this.model.rate.compID || !rateExists) {
           this.model.rate = this.model.collection.getDefaultRate();
         }
-        viewOptions['options'] = this.model.collection.parent.parameters;
+        viewOptions['groupOptions'] = this.getOptions();
         viewOptions['value'] = this.model.rate.compID;
       }
 
@@ -368,9 +385,13 @@ module.exports = View.extend({
   },
   selectRateParam: function (e) {
     let val = e.target.selectedOptions.item(0).value;
-    let param = this.model.collection.parent.parameters.get(val, 'compID');
-    if(param) {
-      this.model.rate = param;
+    console.log(val)
+    var rate = this.model.collection.parent.parameters.get(val, 'compID');
+    if(rate === undefined) {
+      rate = this.model.collection.parent.species.get(val, 'compID');
+    }
+    if(rate) {
+      this.model.rate = rate;
       this.updateViewer();
       this.model.trigger('change-reaction');
       this.model.collection.trigger("change");

client/model-view/views/rule-view.js

@@ -77,14 +77,9 @@ module.exports = View.extend({
   getOptions: function () {
     let species = this.model.collection.parent.species;
     let parameters = this.model.collection.parent.parameters;
-    let specs = species.map(function (specie) {
+    let options = species.map(function (specie) {
       return [specie.compID, specie.name];
     });
-    let params = parameters.map(function (parameter) {
-      return [parameter.compID, parameter.name];
-    });
-    let options = [{groupName: Boolean(specs) ? "Variables" : "Variables (empty)", options: specs},
-                   {groupName: Boolean(params) ? "Parameters" : "Parameters (empty)", options: params}];
     return options;
   },
   removeRule: function () {
@@ -95,21 +90,7 @@ module.exports = View.extend({
   },
   selectRuleVariable: function (e) {
     let species = this.model.collection.parent.species;
-    let parameters = this.model.collection.parent.parameters;
-    let compID = Number(e.target.value);
-    let ruleVar = species.filter(function (specie) {
-      if(specie.compID === compID) {
-        return specie;
-      }
-    });
-    if(!ruleVar.length) {
-      ruleVar = parameters.filter(function (parameter) {
-        if(parameter.compID === compID) {
-          return parameter;
-        }
-      });
-    }
-    this.model.variable = ruleVar[0];
+    this.model.variable = species.get(Number(e.target.value), 'compID')
   },
   update: function (e) {},
   updateValid: function () {},
@@ -152,7 +133,7 @@ module.exports = View.extend({
           name: 'variable',
           required: true,
           idAttributes: 'cid',
-          groupOptions: options,
+          options: options,
           value: this.model.variable.compID
         });
       }

client/model-view/views/specie-view.js

@@ -40,12 +40,19 @@ module.exports = View.extend({
       type: 'booleanAttribute',
       name: 'disabled',
     },
+    'model.observable': {
+      type: function (el, value, previousValue) {
+        el.checked = value;
+      },
+      hook: 'observable'
+    }
   },
   events: {
     'change [data-hook=input-name-container]' : 'setSpeciesName',
     'change [data-hook=specie-mode]' : 'setSpeciesMode',
     'change [data-hook=switching-tol]' : 'setSwitchingType',
     'change [data-hook=switching-min]' : 'setSwitchingType',
+    'change [data-hook=observable]' : 'setObservable',
     'click [data-hook=edit-annotation-btn]' : 'editAnnotation',
     'click [data-hook=remove]' : 'removeSpecie',
     'click [data-hook=collapse-advanced]' : 'changeCollapseButtonText'
@@ -152,6 +159,9 @@ module.exports = View.extend({
       }}
     );
   },
+  setObservable: function (e) {
+    this.model.observable = !this.model.observable;
+  },
   setSpeciesMode: function (e) {
     this.model.mode = e.target.value;
     this.model.collection.trigger('update-species', this.model.compID, this.model, false, false);

client/model-view/views/species-view.js

@@ -46,6 +46,12 @@ module.exports = View.extend({
     this.collection.on('update-species', (compID, specie, isNameUpdate, isDefaultMode) => {
       this.collection.parent.reactions.forEach((reaction) => {
         var changedReaction = false;
+        if(reaction.rate && reaction.rate.compID === compID){
+          reaction.rate = specie;
+          if(reaction.reactionType !== 'custom-propensity') {
+            changedReaction = true;
+          }
+        }
         reaction.reactants.forEach((reactant) => {
           if(reactant.specie.compID === compID) {
             reactant.specie = specie;

client/models/job.js

@@ -74,6 +74,13 @@ module.exports = State.extend({
         // timeZone = timeZone.replace('(', '').replace(')', '') // remove the '()' from the timezone
         return  stamp + hours + ":" + minutes + " " + ampm + " " + timeZone;
       }
+    },
+    sortTime: {
+      deps: ["startTime"],
+      fn: function () {
+        let date = new Date(this.startTime);
+        return Math.round(date.getTime() / 1000);
+      }
     }
   }
 });

client/models/jobs.js

@@ -22,5 +22,6 @@ let Collection = require('ampersand-collection');
 let Job = require('./job');
 
 module.exports = Collection.extend({
-  model: Job
+  model: Job,
+  comparator: 'sortTime'
 });