grnsight 5.0.0 → 5.1.0

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

@@ -1,172 +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
-// by default, this will create tests for the features with included=true in their features.json
-// -l is the option to list the ids you would like to test
-//  `node testing-script-generator.js -l e4 e5 e6` will create tests for e4, e5, e6 features from the table
-// -j is the option to read the test ids from a .json file, default name is testFeatures.json
-// `node testing-script-generator.js -j` will create tests for the ids listed in testFeatures.json
-// `node testing-script-generator.js -j example.json` will create tests for the ids listed in example.json
-
-
-var fs = require("fs");
-var markdownpdf = require("markdown-pdf");
-var moment = require("moment");
-
-// Handle user CLI options
-const options = process.argv.slice(2)
-let toTest = undefined
-if(options.length > 0){
-    if(options[0] == '-l'){
-        toTest = options.slice(1)
-        console.log(toTest)
-    } else if(options[0] == '-j'){
-        const fileName = options[1] ? options[1] : 'testFeatures.json'
-        toTest = JSON.parse(fs.readFileSync(fileName, 'utf-8'))
-    }
-}
-
-// Imports JSON data from data.json
-const JSONFileList = ['edgeFeatures.json', 'fileFeatures.json', 'layoutFeatures.json',
-                'nodeFeatures.json', 'speciesFeatures.json', 'viewFeatures.json', 'viewportFeatures.json']
-var grnsightOptions = JSONFileList.flatMap((fileName)=> JSON.parse(fs.readFileSync(fileName, 'utf8')) )
-// 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 && !toTest) || (toTest && !toTest.includes(test.id)) ) {
-            // 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 && !toTest || toTest && toTest.includes(test.id)) ? "YES" : "NO";
-    var entry = "|" + test.id +"|"+ 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 += "| ID | 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")

package/documents/developer_documents/testing_script_generator/viewFeatures.json

@@ -1,82 +0,0 @@
-[
-    {
-        "id":"v1",
-        "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
-        }
-    },
-    {
-        "id":"v2",
-        "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
-        }
-    },
-    {
-        "id":"v3",
-        "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
-        }
-    },
-    {
-        "id":"v4",
-        "title": "Dropdown Menu: View -> Restrict Graph to Viewport",
-        "text": "The graph 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
-        }
-    },
-    {
-        "id":"v5",
-        "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
-        }
-    }
-]

package/documents/developer_documents/testing_script_generator/viewportFeatures.json

@@ -1,50 +0,0 @@
-[
-    {
-        "id":"vp1",
-        "title": "Viewport Menu: D-Pad Control",
-        "text": "The graph should",
-        "options": {
-            "Click Right Arrow": "shift to the right",
-            "Click Left Arrow": "shift to the left",
-            "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"
-        },
-        "included": false,
-        "availability": {
-            "NoGraphLoaded": false,
-            "WeightedGraphLoaded": true,
-            "UnWeightedGraphLoaded": true
-        }
-    },
-    {
-        "id":"vp2",
-        "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
-        }
-    },
-    {
-        "id":"vp3",
-        "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
-        }
-    }
-]