Model Exploration Settings

client/models/model-exploration-settings.js

@@ -0,0 +1,46 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2020 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+//models
+var State = require('ampersand-state');
+//collections
+var ModelExplorationVariables = require('./model-exploration-variables');
+
+module.exports = State.extend({
+  props: {
+    distributionType: 'string'
+  },
+  collections: {
+    variables: ModelExplorationVariables
+  },
+  initialize: function(attrs, options) {
+    State.prototype.initialize.apply(this, arguments);
+  },
+  updateVariables: function (parameters) {
+    this.variables.forEach(function (variable) {
+      let parameter = parameters.filter(function (parameter) {
+        return parameter.compID === variable.paramID
+      })[0]
+      if(parameter === undefined) {
+        this.removeVariable(variable)
+      }else{
+        variable.updateVariable(variable)
+      }
+    })
+  }
+}); 

client/models/model-exploration-variable.js

@@ -0,0 +1,45 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2020 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+//models
+var State = require('ampersand-state');
+
+module.exports = State.extend({
+  props: {
+    paramID: 'number',
+    min: 'any',
+    max: 'any',
+    steps: 'any',
+    level: 'any',
+    outliers: 'string',
+    seedSize: 'any',
+    hasChangedRanged: 'boolean' 
+  },
+  initialize: function(attrs, options) {
+    State.prototype.initialize.apply(this, arguments);
+  },
+  updateVariable: function (parameter) {
+    let value = parameter.expression
+    if(this.min <= 0 || !this.hasChangedRanged) {
+      this.min = value * 0.5
+    }
+    if(this.max <= 0 || !this.hasChangedRanged) {
+      this.max = value * 1.5
+    }
+  }
+}); 

client/models/model-exploration-variables.js

@@ -0,0 +1,41 @@
+/*
+StochSS is a platform for simulating biochemical systems
+Copyright (C) 2019-2020 StochSS developers.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+//models
+var Variable = require('./model-exploration-variable');
+//collections
+var Collection = require('ampersand-collection');
+
+module.exports = Collection.extend({
+  model: Variable,
+  addVariable: function (paramID) {
+    var variable = this.add({
+      paramID: paramID,
+      min: 0,
+      max: 0,
+      steps: 11,
+      level: 1,
+      outliers: "",
+      seedSize: 1,
+      hasChangedRange: false
+    });
+  },
+  removeVariable: function (variable) {
+    this.remove(variable);
+  }
+});

client/models/settings.js

@@ -20,12 +20,14 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 var State = require('ampersand-state');
 var SimulationSettings = require('./simulation-settings');
 var ParameterSweepSettings = require('./parameter-sweep-settings');
+var ModelExplorationSettings = require('./model-exploration-settings');
 var ResultsSettings = require('./results-settings');
 
 module.exports = State.extend({
   children: {
     simulationSettings: SimulationSettings,
     parameterSweepSettings: ParameterSweepSettings,
+    modelExplorationSettings: ModelExplorationSettings,
     resultsSettings: ResultsSettings
   },
   initialize: function(attrs, options) {

client/pages/workflow-selection.js

@@ -40,7 +40,8 @@ let workflowSelection = PageView.extend({
     "click [data-hook=sciope-model-exploration]" : "notebookWorkflow",
     "click [data-hook=model-inference]" : "notebookWorkflow",
     "click [data-hook=stochss-es]" : "handleEnsembleSimulationClick",
-    "click [data-hook=stochss-ps]" : "handleParameterSweepClick"
+    "click [data-hook=stochss-ps]" : "handleParameterSweepClick",
+    "click [data-hook=stochss-me]" : "handleModelExplorationClick"
   },
   initialize: function (attrs, options) {
     PageView.prototype.initialize.apply(this, arguments);
@@ -147,6 +148,9 @@ let workflowSelection = PageView.extend({
   handleParameterSweepClick: function (e) {
     this.launchStochssWorkflow("parameterSweep")
   },
+  handleModelExplorationClick: function (e) {
+    this.launchStochssWorkflow("modelExploration")
+  },
   launchStochssWorkflow: function (type) {
     let queryString = "?type=" + type + "&path=" + this.modelDir + "&parentPath=" + this.parentPath
     let endpoint = path.join(app.getBasePath(), "stochss/workflow/edit")+queryString

client/templates/includes/modelExplorationSettings.pug

@@ -0,0 +1,36 @@
+div#model-exploration-settings.card.card-body
+
+  div
+
+    h3.inline Model Explorataion Settings
+    button.btn.btn-outline-collapse(data-toggle="collapse", data-target="#collapse-mexplore-settings", data-hook="collapse") -
+
+  div.collapse(class="show", id="collapse-mexplore-settings")
+
+    div.row
+
+      div.col-md-4
+
+        span.inline(for="distribution-type") Distribution Type: 
+
+        div.inline(id="distribution-type" data-hook="distribution-type")
+
+      div.col-md-4(style="display: none")
+
+        span.inline(for="exploration-type") Exploration Type: 
+
+        div.inline(id="exploration-type" data-hook="exploration-type")
+
+      div.col-md-4(style="display: none")
+
+        span.inline(for="feature-extraction") Feature Extraction: 
+
+        div.inline(id="feature-extraction" data-hook="feature-extraction")
+
+    div
+
+      h5 Configure Variable(s)
+
+      div(data-hook="me-variables-collection")
+
+    button.btn.btn-outline-secondary.box-shadow(data-hook="add-me-variable") Add Variable

client/templates/includes/modelExplorationVariable.pug

@@ -0,0 +1,25 @@
+tr
+
+  td: div(data-hook="variable-target")
+
+  td: div(data-hook="target-value")=this.parameter.expression
+
+  td: div(data-hook="variable-min")
+
+  td: div(data-hook="variable-max")
+
+  td
+
+    if(this.distributionType == "Uniform")
+      div(data-hook="variable-steps")
+
+    if(this.distributionType == "Factorial")
+      div(data-hook="variable-level")
+
+    if(this.distributionType == "Latin Hypercube")
+      div(data-hook="variable-seed-size")
+
+  if(this.distributionType == "Factorial")
+    td: div(data-hook="variable-outliers")
+
+  td: button.btn.btn-outline-secondary.box-shadow(data-hook="remove") X

client/templates/includes/modelExplorationVariables.pug

@@ -0,0 +1,40 @@
+table.table
+  thead
+    tr
+      th(scope="col")
+        div
+          div.inline Sweep Target
+
+      th(scope="col")
+        div
+          div.inline Current Value
+
+      th(scope="col")
+        div
+          div.inline Minimum Value
+
+      th(scope="col")
+        div
+          div.inline Maximum Value
+
+      th(scope="col")
+        if(this.distributionType == "Uniform")
+          div
+            div.inline Steps
+
+        if(this.distributionType == "Factorial")
+          div
+            div.inline Level
+
+        if(this.distributionType == "Latin Hypercube")
+          div
+            div.inline Seed Size
+
+      if(this.distributionType == "Factorial")
+        th(scope="col")
+          div
+            div.inline Outliers
+
+      th(scope="col"): div Remove
+
+  tbody(data-hook="me-variables")

client/templates/includes/workflowEditor.pug

@@ -12,6 +12,8 @@ div#workflow-editor.card.card-body
 
     div.collapse(class="show" data-hook="param-sweep-settings-container")
 
+    div.collapse(class="show" data-hook="model-exploration-settings-container")
+
     div(data-hook="sim-settings-container")
 
     div(data-hook="workflow-state-buttons-container")

client/templates/pages/workflowSelection.pug

@@ -31,6 +31,9 @@ section.page
 
           div.tooltip-icon.horizontal-space(data-html="true" data-toggle="tooltip" title=this.tooltips.parameterSweep) <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>
 
+        td
+          button.btn.btn-outline-primary.box-shadow.inline(id="stochss-me" data-hook="stochss-me") Model Exploration
+
   table.table
     thead
       tr