grnsight 4.0.0 → 6.0.0

package/documents/developer_documents/testing_script_generator/featureList.json

@@ -1,496 +0,0 @@
-[
-    {
-        "title": "Load Graph",
-        "text": "GRNsight should",
-        "options": {
-            "None": "have no graph in the viewport",
-            "Dropdown Menu: File -> Open": "lay out a network graph from the Excel workbook if there are no errors in the file",
-            "Dropdown Menu: File -> Import SIF": "lay out a network graph from the SIF file if there are no errors in the file",
-            "Dropdown Menu: File -> Import GraphML": "lay out a network graph from the GraphML file if there are no errors in the file",
-            "Dropdown Menu: Demo -> Demo #1": "lay out an unweighted network graph from Demo #1",
-            "Dropdown Menu: Demo -> Demo #2": "lay out a weighted network graph from Demo #2",
-            "Dropdown Menu: Demo -> Demo #3": "lay out an unweighted network graph from Demo #3",
-            "Dropdown Menu: Demo -> Demo #4": "lay out a weighted network graph from Demo #4"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: File -> Reload",
-        "text": "The graph should",
-        "options": {
-            "Select": "center, zoom to 100%, and reapply the force graph parameters"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: File -> Export Data",
-        "text": "GRNsight should",
-        "options": {
-            "Select \"To Unweighted SIF\"": "export an unweighted SIF file from the graph currently loaded",
-            "Select \"To Weighted SIF\"": "export a weighted SIF file from the graph currently loaded",
-            "Select \"To Unweighted GraphML\"": "export an unweighted GraphML file from the graph currently loaded",
-            "Select \"To Weighted GraphML\"": "export a weighted GraphML file from the graph currently loaded"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: File -> Print",
-        "text": "GRNsight should",
-        "options": {
-            "Select": "open the Print Dialogue Box"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Help",
-        "text": "GRNsight should",
-        "options": {
-            "Select \"Getting Started\"": "open the GRNsight documentation page",
-            "Select \"GRNsight Wiki\"": "open the GRNsight wiki page",
-            "Select \"About GRNsight\"": "open the About GRNsight page"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Force Graph Parameter Sliders",
-        "text": "",
-        "options": {
-            "Keep at Default Values": "The graph should be laid out according to the default values of the force graph parameter sliders",
-            "Decrease Link Distance": "The graph's edges should visibly decrease in length if Lock Force Graph Parameters is unchecked",
-            "Increase Link Distance": "The graph's edges should visibly increase in length if Lock Force Graph Parameters is unchecked",
-            "Increase Charge": "The graph's nodes should visibly increase attraction to each other if Lock Force Graph Parameters is unchecked",
-            "Decrease Charge": "The graph's nodes should visibly decrease attraction to each other if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Lock Force Graph Parameters Checkbox",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Check": "be disabled.",
-            "Uncheck": "be enabled."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Reset Force Graph Parameters Button",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Click": "revert to the default values, if Lock Force Graph Parameters is unchecked."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Undo Reset Button",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-            "Click": "return to the values they had before the Undo Reset button (or menu item) was selected, if the Undo Reset button is enabled."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title" : "Sidebar Menu: Restrict Graph to Viewport Checkbox",
-        "text": "The graph bounding box should",
-        "options" : {
-            "Check": "always be contained within the viewport.",
-            "Uncheck": "be allowed to extend past the viewport"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Viewport Size",
-        "text": "",
-        "options": {
-            "Keep as Detected": "Upon loading or reloading the GRNsight webpage, the viewport size should be automatically detected and set to small, medium, or large, based on the size of the browser window.",
-            "Select \"Small\"": "The viewport size should be set to small",
-            "Select \"Medium\"": "The viewport size should be set to medium",
-            "Select \"Large\"": "The viewport size should be set to large",
-            "Select \"Fit to Window\"": "The viewport size should automatically be set to the size of the browser window"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Edge",
-        "text": "GRNsight should",
-        "options": {
-            "Select \"Format edges based on optimized weight parameters\"": "format edges based on optimized weight parameters",
-            "Select \"Default to black edges with regular arrowheads\"": "default to black edges with regular arrowheads"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Hide/Show Edge Weights",
-        "text": "",
-        "options": {
-            "Select \"Show With Mouse Over\"": "A single edge weight should display when user mouses over a single edge.",
-            "Select \"Always Show Edge Weights\"": "All edge weights should always be visible.",
-            "Select \"Never Show Edge Weights\"": "No edge weights should be visible."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Dropdown Menu: Edge -> Hide/Show Edge Weights",
-        "text": "",
-        "options": {
-            "Check \"Show With Mouse Over\"": "A single edge weight should display when user mouses over a single edge.",
-            "Check \"Always Show Edge Weights\"": "All edge weights should always be visible.",
-            "Check \"Never Show Edge Weights\"": "No edge weights should be visible."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Sidebar Menu: Edge Weight Normalization Factor",
-        "text": "The graph should",
-        "options": {
-            "Enter a Number in the Box and Click \"Set Factor\" button": "reload with the new normalization factor applied to its edge weight thicknesses"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Dropdown Menu: Edge -> Edge Weight Normalization Factor",
-        "text": "The graph should",
-        "options": {
-            "Enter a Number in the Box and Press Enter": "reload with the new normalization factor applied to its edge weight thicknesses"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Sidebar Menu: Reset Factor Button",
-        "text": "The graph should",
-        "options": {
-            "Click": "reset to its default normalization factor and reload the graph"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Dropdown Menu: Edge -> Reset Edge Weight Normalization",
-        "text": "The graph should",
-        "options": {
-            "Click": "reset to its default normalization factor and reload the graph"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Sidebar Menu: Gray Threshold Slider",
-        "text": "The graph should reload, with",
-        "options": {
-            "Change the Grey Threshold Value": "edges that fall below the threshold value colored gray"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Dropdown Menu: Edge -> Gray Threshold Input Box",
-        "text": "The graph should reload, with",
-        "options": {
-            "Change the Grey Threshold Value and Press Enter": "edges that fall below the threshold value colored gray"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Sidebar Menu: Show Grey Edges as Dashed Checkbox",
-        "text": "The graph should",
-        "options": {
-            "Uncheck": "show gray lines as solid lines",
-            "Check": "show gray lines as dashed lines"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Dropdown Menu: Edge -> Show Grey Edges as Dashed",
-        "text": "The graph should",
-        "options": {
-            "Uncheck": "show gray lines as solid lines",
-            "Check": "show gray lines as dashed lines"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": false }
-    },
-    {
-        "title": "Viewport Menu: D-Pad Control",
-        "text": "The graph should",
-        "options": {
-            "Click Right Arrow": "shift to the left",
-            "Click Left Arrow": "shift to the right",
-            "Click Up Arrow": "shift down",
-            "Click Down Arrow": "shift up",
-            "Click Center Button": "move to the center of the bounding box (note that it is not the same thing as the viewport"
-        },
-        "conditional": "if \"Restrict Graph to Viewport\" is Unchecked.",
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Viewport Menu: Zoom Slider",
-        "text": "The graph should",
-        "options": {
-            "Increase Zoom Level": "zoom in (get larger)",
-            "Decrease Zoom Level": "zoom out (get smaller)"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Top Dataset",
-        "text": "The top half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the first expression dataset detected in the input workbook",
-            "Select Top Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Node -> Select Top Dataset",
-        "text": "The top half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the first expression dataset detected in the input workbook",
-            "Check New Top Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Bottom Dataset",
-        "text": "The bottom half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the same dataset as the top dataset",
-            "Select Bottom Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Node -> Select Bottom Dataset",
-        "text": "The bottom half of each node should be colored using data from",
-        "options": {
-            "Keep Default Selection": "the same dataset as the top dataset",
-            "Check New Bottom Dataset from Dropdown List": "the selected dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Log Fold Change Max Value",
-        "text": "The node coloring visualization's color intensity should",
-        "options": {
-            "Keep Default Value": "default to having a Log Fold Change Max Value of 3",
-            "Increase Log Fold Change Max Value": "decrease",
-            "Decrease Log Fold Change Max Value": "increase"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Node -> Log Fold Change Max Value",
-        "text": "The node coloring visualization's color intensity should",
-        "options": {
-            "Keep Default Value": "default to having a Log Fold Change Max Value of 3",
-            "Increase Log Fold Change Max Value": "decrease",
-            "Decrease Log Fold Change Max Value": "increase"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Average Replicates Values (Top Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for top dataset",
-            "Uncheck": "not average replicate values for top dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Node -> Average Replicates Values (Top Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for top dataset",
-            "Uncheck": "not average replicate values for top dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Average Replicates Values (Bottom Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for bottom dataset",
-            "Uncheck": "not average replicate values for bottom dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Node -> Average Replicates Values (Bottom Dataset)",
-        "text": "GRNsight should",
-        "options": {
-            "Check": "average replicate values for bottom dataset",
-            "Uncheck": "not average replicate values for bottom dataset"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Node Coloring Toggle Button",
-        "text": "",
-        "options": {
-            "Click": "Node coloring should toggle between on and off, with default being on and button text should toggle between 'Enable Node Coloring' and 'Disable Node Coloring'"
-        },
-        "included": false,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Node -> Disable Node Coloring",
-        "text": "",
-        "options": {
-            "Check": "Node coloring should become disabled, and Node Coloring Toggle Button text in sidebar menu should read 'Enable Node Coloring'",
-            "Uncheck": "Node coloring should become enabled, and Node Coloring Toggle Button text in sidebar menu should read 'Disable Node Coloring'"
-        },
-        "included": true,
-        "conditional": "if expression data sheets are present in input workbook",
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Sidebar Menu: Grid Layout",
-        "text": "The graph should",
-        "options": {
-            "Keep at Default": "default to force graph layout",
-            "Click Grid Layout Button": "change to grid layout",
-            "Click Force Graph Layout Button": "change to force graph layout"
-        },
-        "included": true,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: View -> Viewport Size",
-        "text": "",
-        "options": {
-            "Keep as Detected": "Upon loading or reloading the GRNsight webpage, the viewport size should be automatically detected and set to small, medium, or large, based on the size of the browser window.",
-            "Check \"Small\"": "The viewport size should be set to small",
-            "Check \"Medium\"": "The viewport size should be set to medium",
-            "Check \"Large\"": "The viewport size should be set to large",
-            "Check \"Fit to Window\"": "The viewport size should automatically be set to the size of the browser window"
-        },
-        "included": true,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: View -> Restrict Graph to Viewport",
-        "text": "The viewport should",
-        "options": {
-            "Check": "always be contained within the viewport.",
-            "Uncheck": "be allowed to extend past the viewport"
-        },
-        "included": true,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: View -> Zoom",
-        "text": "The viewport should",
-        "options": {
-            "Enter Zoom Value, then Press Enter": "should zoom according to the value"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Layout -> Graph Options",
-        "text": "The graph should",
-        "options": {
-            "Keep at Default": "be in force graph layout by default",
-            "Grid Layout": "apply grid layout",
-            "Force Graph": "apply force graph layout"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Layout -> Lock Force Graph Parameters",
-        "text": "The Force Graph Parameter sliders should",
-        "options": {
-          "Check \"Lock Force Graph Parameters\"": "be disabled.",
-          "Uncheck \"Lock Force Graph Parameters\"": "be enabled."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Layout -> Reset Force Graph Parameters",
-        "text": "The force graph parameters should",
-        "options": {
-            "Click \"Reset Force Graph Parameters\"": "revert to the default values, if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Layout -> Undo Reset",
-        "text": "The force graph parameters should",
-        "options": {
-            "Click \"Undo Reset\"": "return to the values they had before the Undo Reset button (or menu item) was selected, if Undo Reset is enabled."
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Layout -> Link Distance",
-        "text": "",
-        "options": {
-            "Input Value, then Press Enter": "The graph's edges should visibly change in length to the value entered if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Dropdown Menu: Layout -> Charge",
-        "text": "",
-        "options": {
-            "Input Value, then Press Enter": "The graph's nodes should visibly change it's level of attraction to each other to the value entered if Lock Force Graph Parameters is unchecked"
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": true, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    },
-    {
-        "title": "Viewport Menu: Node",
-        "text": "",
-        "options": {
-            "No Click": "",
-            "Right Click": "Gene information page should appear in a new tab within the browser.",
-        },
-        "included": false,
-        "availability": {"NoGraphLoaded": false, "WeightedGraphLoaded": true, "UnWeightedGraphLoaded": true }
-    }
-]

package/documents/developer_documents/testing_script_generator/testing-script-generator.js

@@ -1,149 +0,0 @@
-// Instructions for generating new testing document:
-// Make any changes in the data.json file
-// Navigate to documents>developer_documents>testing-script-generator folder on the command line
-// Run node testing-script-generator.js to generate new Testing Document file
-
-var fs = require("fs");
-var markdownpdf = require("markdown-pdf");
-var moment = require("moment");
-
-// Imports JSON data from data.json
-var grnsightOptions = JSON.parse(fs.readFileSync('featureList.json', 'utf8'));
-
-// Node class for representing each test
-class Node {
-    constructor (instructions, results) {
-        this.instructions = instructions || [];
-        this.results = results || [];
-    }
-    addResult (result) {
-        this.results.push(result);
-    }
-    addInstruction(instruction) {
-        this.instructions.push(instruction);
-    }
-    print() {
-        var string = "";
-        string += "Instructions:\n";
-        this.instructions.forEach(function(instruction) {
-            string += "- " + instruction + "\n";
-        });
-        string += "\nResults:\n";
-        this.results.forEach(function (result) {
-            string += "- " + result + "\n";
-        });
-        return string;
-    }
-}
-
-// Initially, arrayOfNodes only contains an empty node
-var root = new Node();
-var arrayOfNodes = [root];
-var testDescription = "";
-var availabilityDescription = "";
-
-var addChildren = function (arrayOfNodes, optionKeys, test) {
-    var newArrayOfNodes = [];
-    // Loops through each node in arrayOfNodes
-    arrayOfNodes.forEach(function(node) {
-        if (!test.included) {
-            // Skip this test by adding the original node itself to the newArrayOfNodes
-            newArrayOfNodes.push(node);
-        } else {
-            optionKeys.forEach(function(option) {
-                var instruction = test.title + " - " + option;
-                var result = test.text + " " + test.options[option];
-                result = test.conditional ? result + ", " + test.conditional : result;
-                var newNode = new Node();
-                // The null option is equivalent to disabling the test.
-                if (option !== "NULL") {
-                    // Adds the new instruction / result pair only
-                    newNode.addInstruction(instruction);
-                    newNode.addResult(result);
-                }
-                // The newNode inherits all of the parent's instruction / result pairs
-                for (var i = 0; i < node.instructions.length; i++) {
-                    newNode.addInstruction(node.instructions[i]);
-                    newNode.addResult(node.results[i]);
-                }
-                newArrayOfNodes.push(newNode);
-            });
-        }
-    });
-    return newArrayOfNodes;
-}
-
-// Performs the combinatorics for each GRNsight option.
-for (var i = grnsightOptions.length - 1; i >=0; i--) {
-    var test = grnsightOptions[i];
-    var optionKeys = Object.keys(test.options);
-    arrayOfNodes = addChildren(arrayOfNodes, optionKeys, test);
-}
-
-// Formats the table to display all the GRNsight options, user interactions, and results.
-grnsightOptions.forEach(function(test) {
-    var optionKeys = Object.keys(test.options);
-    var entry = "|" + test.title + "|";
-    var status = test.included ? "YES" : "NO";
-    var entry = "|" + status + " | " + test.title + "|";
-    var noGraphLoadedAvailability = test.availability['NoGraphLoaded'] ? "YES": "NO";
-    var weightedGraphLoadedAvailability = test.availability['WeightedGraphLoaded'] ? "YES": "NO";
-    var unweightedGraphLoadedAvailability = test.availability['UnWeightedGraphLoaded'] ? "YES": "NO";
-    var availability = `| ${noGraphLoadedAvailability} | ${weightedGraphLoadedAvailability} | ${unweightedGraphLoadedAvailability} | `
-    optionKeys.forEach(function(option) {
-        var result = test.text + " " + test.options[option];
-        result = test.conditional ? result + ", " +  test.conditional : result;
-        testDescription += entry + option +  " | " + result + "|\n";
-        availabilityDescription += `| ${test.title} - ${option} ${availability}\n`
-    });
-});
-
-// Generates the markdown document, combining the table with the test listing
-var formatMarkdown = function (arrayOfNodes) {
-    var md = "## GRNsight Client Side Testing Overview";
-    md += "\nLast Updated: " + moment().format("YYYY-MM-DD");
-    md += "\n\n";
-    md += "| Included in Testing Protocol  | GRNsight Option |  User Action | Result | \n"
-    md += "| --------------- | ------ | ------- | ------ | \n"
-    md += testDescription;
-    md += formatFunctionAvailabilityTable();
-    md += "\n## Client Side Tests\n";
-    for (var i = 0; i < arrayOfNodes.length; i++) {
-        md += "### Test " + (i + 1) + "\n";
-        md += arrayOfNodes[i].print() + "\n";
-    }
-    return md;
-}
-
-var formatFunctionAvailabilityTable = function() {
-    var md = "\n## GRNsight Function Availability Table";
-    md += "\n\n";
-    md += "| GRNsight Function | No Graph Loaded | Weighted Graph Loaded | Unweighted Graph Loaded  | \n";
-    md += "|  ---------------- | --------------- | ----------------------- | ---------------------- | \n";
-    md += availabilityDescription;
-    return md;
-}
-
-var markdownDocument = formatMarkdown(arrayOfNodes);
-// var functionAvailability = formatFunctionAvailabilityTable();
-
-// Writes over the GRNsightTestingDocument.md file
-fs.writeFile('GRNsightTestingDocument.md', markdownDocument, function (err) {
-  if (err) return console.log(err);
-});
-
-// Generates the GRNsight Function Availability Markdown file
-// fs.writeFile("GRNsightFunctionAvailability.md", functionAvailability, function (err) {
-//     if (err) return console.log(err);
-// })
-
-markdownpdf().from("GRNsightTestingDocument.md").to("GRNsightTestingDocument.pdf", function () {
-  console.log("Created GRNsightTestingDocument.pdf");
-})
-
-// markdownpdf().from("GRNsightFunctionAvailability.md").to("GRNsightFunctionAvailability.pdf", function () {
-//   console.log("Created GRNsightFunctionAvailability.pdf");
-// })
-
-console.log("\nGRNsightTestingDocument.md has been successfully regenerated, and includes " + arrayOfNodes.length + " tests.");
-console.log("Update the wiki by copy/pasting Markdown code to: https://github.com/dondi/GRNsight/wiki/Client-Side-Testing-Document\n")