grnsight 3.0.0 → 5.1.0

package/test/graph-library-tests.js

@@ -1,165 +0,0 @@
-/* eslint-disable max-len */
-var assert = require("chai").assert;
-var xlsx = require("node-xlsx");
-var cytoscape = require("cytoscape");
-var test = require("./test");
-var spreadsheetController = require(__dirname + "/../server/controllers" + "/spreadsheet-controller")();
-
-// NOTE: Temporarily skipped out pending resolution of #474, and other related issues
-describe.skip("graph-library-tests", function () {
-    describe("basic-cytoscape-conversion", function () {
-        it("convert to cytoscape correctly", function () {
-            var input = "test-files/graph-statistics-tests/graph-stats-demo.xlsx";
-            var sheet = xlsx.parse(input);
-            var network = spreadsheetController.parseSheet(sheet);
-            // var cytoscapeElements = grnSightToCytoscape(network);
-            var cytoscapeElements = spreadsheetController.grnSightToCytoscape(network);
-
-            /* eslint-disable no-unused-vars */
-            // require calls cytoscape as a function so the below code is needed to call cytoscape
-            var cy = cytoscape({
-                headless: true,
-                elements: cytoscapeElements
-            });
-            /* eslint-enable no-unused-vars */
-
-            assert.equal(cytoscapeElements.length, 13);
-
-            assert.equal(cytoscapeElements[0].data.id, "a");
-            assert.equal(cytoscapeElements[1].data.id, "b");
-            assert.equal(cytoscapeElements[2].data.id, "c");
-            assert.equal(cytoscapeElements[3].data.id, "d");
-            assert.equal(cytoscapeElements[4].data.id, "e");
-            assert.equal(cytoscapeElements[5].data.id, "f");
-
-            assert.equal(cytoscapeElements[6].data.id, "aa");
-            assert.equal(cytoscapeElements[7].data.id, "ba");
-            assert.equal(cytoscapeElements[8].data.id, "cb");
-            assert.equal(cytoscapeElements[9].data.id, "db");
-            assert.equal(cytoscapeElements[10].data.id, "ec");
-            assert.equal(cytoscapeElements[11].data.id, "fd");
-            assert.equal(cytoscapeElements[12].data.id, "de");
-
-        });
-    });
-
-    describe("shortest path", function () {
-        it("returns the undirected shortest path from f to b in graph-stats-demo", function () {
-            test.shortestPath("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "f", "b", 2);
-        });
-
-        it("returns the directed shortest path from f to b in graph-stats-demo", function () {
-            test.shortestPath("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "f", "b", 2);
-        });
-
-        it("returns the undirected shortest path from b to f in graph-stats-demo", function () {
-            test.shortestPath("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "b", "f", 2);
-        });
-
-        it("returns the directed shortest path from b to f in graph-stats-demo", function () {
-            test.shortestPath("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "b", "f", Infinity);
-        });
-
-        it("returns the undirected shortest path from f to b in 75-genes-150-edges", function () {
-            this.timeout(10000);
-            test.shortestPath("test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx", false, "CDC28", "ADA2", 3);
-        });
-
-        it("returns the directed shortest path from f to b in 75-genes-150-edges", function () {
-            this.timeout(10000);
-            test.shortestPath("test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx", true, "CDC28", "ADA2", Infinity);
-        });
-
-        it("returns the undirected shortest path from f to b in 10-genes-max-edges", function () {
-            test.shortestPath("test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx", false, "DAL80", "ECM22", 1);
-        });
-
-        it("returns the directed shortest path from f to b in 10-genes-max-edges", function () {
-            test.shortestPath("test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx", true, "DAL80", "ECM22", 1);
-        });
-
-        it("returns the undirected shortest path from f to b in 12-genes-max-edges", function () {
-            test.shortestPath("test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx", false, "DAL80", "ECM22", 1);
-        });
-
-        it("returns the directed shortest path from f to b in 12-genes-max-edges", function () {
-            test.shortestPath("test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx", true, "DAL80", "ECM22", 1);
-        });
-    });
-
-    describe("betweenness centrality", function () {
-        it("returns the undirected betweenness centrality of a in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "a", 0);
-        });
-
-        it("returns the directed betweenness centrality of a in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "a", 0);
-        });
-
-        it("returns the undirected betweenness centrality of b in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "b", 11);
-        });
-
-        it("returns the directed betweenness centrality of b in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "b", 11);
-        });
-
-        it("returns the undirected betweenness centrality of c in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "c", 2);
-        });
-
-        it("returns the directed betweenness centrality of c in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "c", 2);
-        });
-
-        it("returns the undirected betweenness centrality of d in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "d", 11);
-        });
-
-        it("returns the directed betweenness centrality of d in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "d", 11);
-        });
-
-        it("returns the undirected betweenness centrality of e in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "e", 2);
-        });
-
-        it("returns the directed betweenness centrality of e in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "e", 2);
-        });
-
-        it("returns the undirected betweenness centrality of f in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", false, "f", 0);
-        });
-
-        it("returns the directed betweenness centrality of f in graph-stats-demo", function () {
-            test.betweennessCentrality("test-files/graph-statistics-tests/graph-stats-demo.xlsx", true, "f", 0);
-        });
-
-        it("returns the undirected betweenness centrality of f in 75-genes-150-edges", function () {
-            this.timeout(10000);
-            test.betweennessCentrality("test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx", false, "CDC28", 171.50351735503662);
-        });
-
-        it("returns the directed betweenness centrality of f in 75-genes-150-edges", function () {
-            this.timeout(10000);
-            test.betweennessCentrality("test-files/graph-tests/different-sized-networks/75-genes-150-edges.xlsx", true, "CDC28", 171.50351735503662);
-        });
-
-        it("returns the undirected betweenness centrality of f in 10-genes-max-edges", function () {
-            test.betweennessCentrality("test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx", false, "DAL80", 0);
-        });
-
-        it("returns the directed betweenness centrality of f in 10-genes-max-edges", function () {
-            test.betweennessCentrality("test-files/graph-tests/different-sized-networks/10-genes-max-edges.xlsx", true, "DAL80", 0);
-        });
-
-        it("returns the undirected betweenness centrality of f in 12-genes-max-edges", function () {
-            test.betweennessCentrality("test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx", false, "DAL80", 0);
-        });
-
-        it("returns the directed betweenness centrality of f in 12-genes-max-edges", function () {
-            test.betweennessCentrality("test-files/graph-tests/different-sized-networks/12-genes-max-edges.xlsx", true, "DAL80", 0);
-        });
-    });
-});

package/web-client/public/js/container.js

@@ -1,121 +0,0 @@
-/* eslint no-unused-vars: [2, {"varsIgnorePattern": "grnTest|enableScroll|manualZoom"}] */
-export const container = function () {
-    var grnTest = $(".grnTest");
-    var container = $(".grnsight-container");
-    var enableScroll = $("#enableScroll");
-    var pageWidth = $(window).width();
-
-    var WIDTH_OFFSET = 250;
-    var HEIGHT_OFFSET = 53;
-
-    var MEDIUM_PAGE_WIDTH = 1500;
-    var LARGE_PAGE_WIDTH = 2200;
-
-
-    var windowWidth = $(window).width() - WIDTH_OFFSET;
-    var windowHeight = $(window).height() - HEIGHT_OFFSET;
-
-    if (pageWidth < MEDIUM_PAGE_WIDTH) {
-        $("#boundBoxS").prop("checked", true);
-        container.addClass("containerS");
-    } else if (pageWidth > MEDIUM_PAGE_WIDTH && pageWidth < LARGE_PAGE_WIDTH) {
-        $("#boundBoxM").prop("checked", true);
-        container.addClass("containerM");
-    } else {
-        $("#boundBoxL").prop("checked", true);
-        container.addClass("containerL");
-    }
-
-    var setSizeIndicator = function (selector) {
-        $("#viewport-size-s span, #viewport-size-m span, #viewport-size-l span, #viewport-size-fit span")
-          .removeClass("glyphicon-ok");
-        $(selector).addClass("glyphicon-ok");
-    };
-
-    var small = function () {
-        setSizeIndicator("#viewport-size-s span");
-    };
-
-    var medium = function () {
-        setSizeIndicator("#viewport-size-m span");
-    };
-
-    var large = function () {
-        setSizeIndicator("#viewport-size-l span");
-    };
-
-    var fit = function () {
-        setSizeIndicator("#viewport-size-fit span");
-    };
-
-    $("#viewport-size-s").on("click", function () {
-        $("#boundBoxS").prop("checked", true).trigger("click");
-        small();
-    });
-
-    $("#boundBoxS").on("click", function () {
-        $("#boundBoxS").prop("checked", true);
-        small();
-    });
-
-    $("#viewport-size-m").on("click", function () {
-        $("#boundBoxM").prop("checked", true).trigger("click");
-        medium();
-    });
-
-    $("#boundBoxM").on("click", function () {
-        $("#viewport-size-m").prop("checked", true);
-        medium();
-    });
-
-    $("#viewport-size-l").on("click", function () {
-        $("#boundBoxL").prop("checked", true).trigger("click");
-        large();
-    });
-
-    $("#boundBoxL").on("click", function () {
-        $("#viewport-size-l").prop("checked", true);
-        large();
-    });
-
-    $("#viewport-size-fit").on("click", function () {
-        $("#boundBoxFit").prop("checked", true).trigger("click");
-        fit();
-    });
-
-    $("#boundBoxFit").on("click", function () {
-        $("#viewport-size-fit").prop("checked", true);
-        fit();
-    });
-
-    $("#restrict-graph-to-viewport").on("click", function () {
-        if ($(".viewport").prop("checked")) {
-            $("#restrict-graph-to-viewport span").removeClass("glyphicon-ok");
-            $(".viewport").prop("checked", false);
-            $(".viewport").trigger("change");
-        } else {
-            $("#restrict-graph-to-viewport span").addClass("glyphicon-ok");
-            $(".viewport").prop("checked", true).trigger("change");
-        }
-    });
-
-
-    $(".boundBoxSize").on("click", function () {
-        var currentValue = $(this).val();
-        var grnsightContainerClass = "grnsight-container " + currentValue;
-        if (!container.hasClass(currentValue)) {
-            container.attr("class", grnsightContainerClass);
-            container.css(currentValue === "containerFit" ? {width: windowWidth, height: windowHeight} :
-            {width: "", height: ""});
-        }
-    });
-
-    $(window).on("resize", function () {
-        windowWidth = $(window).width() - WIDTH_OFFSET;
-        windowHeight = $(window).height() - HEIGHT_OFFSET;
-        if (container.hasClass("containerFit")) {
-            container.css({width: windowWidth, height: windowHeight});
-        }
-    });
-
-};

package/web-client/public/js/node-coloring.js

@@ -1,306 +0,0 @@
-var MINIMUM_MAX_LOG_FOLD_CHANGE = -100;
-var MAXIMUM_MAX_LOG_FOLD_CHANGE = 100;
-var DEFAULT_MAX_LOG_FOLD_CHANGE = 3;
-var MAX_NUM_CHARACTERS_DROPDOWN = 24;
-
-var NODE_COLORING_MENU = ".node-coloring";
-
-var BOTTOM_DATASET_SELECTION_SIDEBAR = "#dataset-bottom";
-var TOP_DATASET_SELECTION_SIDEBAR = "#dataset-top";
-var NODE_COLORING_TOGGLE_SIDEBAR = "#nodeColoringToggle";
-var AVG_REPLICATE_VALS_BOTTOM_SIDEBAR = "#averageDataBottom";
-var AVG_REPLICATE_VALS_TOP_SIDEBAR = "#averageDataTop";
-
-var AVG_REPLICATE_VALS_TOP_MENU = "#averageDataTopMenu";
-var AVG_REPLICATE_VALS_BOTTOM_MENU = "#averageDataBottomMenu";
-var NODE_COLORING_TOGGLE_MENU = "#node-coloring-toggle-menu";
-var TOP_DATASET_SELECTION_MENU = "#topDatasetDropdownMenu";
-var BOTTOM_DATASET_SELECTION_MENU = "#bottomDatasetDropdownMenu";
-
-var NODE_COLORING_TOGGLE_CLASS = ".nodeColoringToggle";
-var LOG_FOLD_CHANGE_MAX_VALUE_CLASS = ".logFoldChangeMaxValue";
-var LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_BUTTON = "#log-fold-change-button";
-
-
-var endsInExpressionRegExp = /expression$/;
-
-var shortenExpressionSheetName = function (name) {
-    return (name.length > MAX_NUM_CHARACTERS_DROPDOWN) ?
-      (name.slice(0, MAX_NUM_CHARACTERS_DROPDOWN) + "...") : name;
-};
-
-export var hasExpressionData = function (sheets) {
-    for (var property in sheets) {
-        if (property.match(endsInExpressionRegExp)) {
-            return true;
-        }
-    }
-    return false;
-};
-
-export var nodeColoringController = {
-
-    // renderNodeColoring: function () { }, // defined in graph.js
-    // removeNodeColoring: function () { }, // defined in graph.js
-
-    updateAverageReplicateValuesTopDataset: function (averageTopDataset) {
-        if (averageTopDataset) {
-            $(AVG_REPLICATE_VALS_TOP_MENU + " span").addClass("glyphicon-ok");
-            $(AVG_REPLICATE_VALS_TOP_MENU).prop("checked", "checked");
-            $(AVG_REPLICATE_VALS_TOP_SIDEBAR).prop("checked", "checked");
-        } else {
-            $(AVG_REPLICATE_VALS_TOP_MENU + " span").removeClass("glyphicon-ok");
-            $(AVG_REPLICATE_VALS_TOP_MENU).removeProp("checked");
-            $(AVG_REPLICATE_VALS_TOP_SIDEBAR).removeProp("checked");
-        }
-        this.avgTopDataset = averageTopDataset;
-        this.renderNodeColoring();
-    },
-
-    updateAverageReplicateValuesBottomDataset: function (averageBottomDataset) {
-        if (averageBottomDataset) {
-            $(AVG_REPLICATE_VALS_BOTTOM_MENU + " span").addClass("glyphicon-ok");
-            $(AVG_REPLICATE_VALS_BOTTOM_MENU).prop("checked", "checked");
-            $(AVG_REPLICATE_VALS_BOTTOM_SIDEBAR).prop("checked", "checked");
-        } else {
-            $(AVG_REPLICATE_VALS_BOTTOM_MENU + " span").removeClass("glyphicon-ok");
-            $(AVG_REPLICATE_VALS_BOTTOM_MENU).removeProp("checked");
-            $(AVG_REPLICATE_VALS_BOTTOM_SIDEBAR).removeProp("checked");
-        }
-        this.avgBottomDataset = averageBottomDataset;
-        this.renderNodeColoring();
-    },
-
-    disableNodeColoring: function () {
-        $(NODE_COLORING_TOGGLE_MENU + " span").addClass("glyphicon-ok");
-        $(NODE_COLORING_TOGGLE_SIDEBAR).val("Enable Node Coloring");
-        this.nodeColoringEnabled = false;
-        this.removeNodeColoring();
-    },
-
-    enableNodeColoring: function () {
-        $(NODE_COLORING_TOGGLE_MENU + " span").removeClass("glyphicon-ok");
-        $(NODE_COLORING_TOGGLE_SIDEBAR).val("Disable Node Coloring");
-        this.nodeColoringEnabled = true;
-        this.renderNodeColoring();
-    },
-
-    updateLogFoldChangeMaxValue: function (value) {
-        $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(value);
-        this.logFoldChangeMaxValue = value;
-        this.renderNodeColoring();
-    },
-
-    updateTopDataset: function (selection) {
-        $(TOP_DATASET_SELECTION_SIDEBAR).val(selection);
-        this.removeAllChecksFromMenuDatasetOptions(TOP_DATASET_SELECTION_MENU);
-        $(`${TOP_DATASET_SELECTION_MENU} li[value='${selection}'] a span`).addClass("glyphicon-ok");
-
-        this.topDataset = selection;
-        if (this.bottomDataSameAsTop) {
-            this.bottomDataset = selection;
-        }
-        this.renderNodeColoring();
-    },
-
-    updateBottomDataset: function (selection) {
-        $(BOTTOM_DATASET_SELECTION_SIDEBAR).val(selection);
-        this.removeAllChecksFromMenuDatasetOptions(BOTTOM_DATASET_SELECTION_MENU);
-        $(`${BOTTOM_DATASET_SELECTION_MENU} li[value='${selection}'] a span`).addClass("glyphicon-ok");
-
-        if (selection === "Same as Top Dataset") {
-            this.bottomDataset = this.topDataset;
-            this.bottomDataSameAsTop = true;
-        } else {
-            this.bottomDataSameAsTop = false;
-            this.bottomDataset = selection;
-        }
-        this.renderNodeColoring();
-    },
-
-    removeAllChecksFromMenuDatasetOptions: function (id) {
-        $(`${id} li a span`).each(
-            function () {
-                $(this).removeClass("glyphicon-ok");
-            }
-        );
-    },
-
-    logFoldChangeMaxValueInputValidation: function (value) {
-        if (value === "" || value === "0") {
-            return DEFAULT_MAX_LOG_FOLD_CHANGE;
-        } else if (value < MINIMUM_MAX_LOG_FOLD_CHANGE) {
-            return MINIMUM_MAX_LOG_FOLD_CHANGE;
-        } else if (value > MAXIMUM_MAX_LOG_FOLD_CHANGE) {
-            return MAXIMUM_MAX_LOG_FOLD_CHANGE;
-        } else {
-            return value;
-        }
-    },
-
-    configureNodeColoringHandlers: function () {
-        $(AVG_REPLICATE_VALS_TOP_SIDEBAR).on("change", {handler: this}, function (event) {
-            event.data.handler.updateAverageReplicateValuesTopDataset($(this).prop("checked"));
-        });
-
-        $(AVG_REPLICATE_VALS_TOP_MENU).on("click", {handler: this}, function (event) {
-            event.data.handler.updateAverageReplicateValuesTopDataset(!$(this).prop("checked"));
-        });
-
-        $(AVG_REPLICATE_VALS_BOTTOM_SIDEBAR).on("change", {handler: this}, function (event) {
-            event.data.handler.updateAverageReplicateValuesBottomDataset($(this).prop("checked"));
-        });
-
-        $(AVG_REPLICATE_VALS_BOTTOM_MENU).on("click", {handler: this}, function (event) {
-            event.data.handler
-              .updateAverageReplicateValuesBottomDataset(!$(AVG_REPLICATE_VALS_BOTTOM_MENU).prop("checked"));
-        });
-
-        $(NODE_COLORING_TOGGLE_CLASS).on("click", {handler: this}, function (event) {
-            event.data.handler.nodeColoringEnabled ?
-                event.data.handler.disableNodeColoring() : event.data.handler.enableNodeColoring();
-        });
-
-        $(LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_BUTTON).on("click", {handler: this}, function (event) {
-            var validated = event.data.handler
-                .logFoldChangeMaxValueInputValidation($("#log-fold-change-max-value-menu").val());
-            event.data.handler.updateLogFoldChangeMaxValue(validated);
-        });
-
-        $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).on("change", {handler: this}, function (event) {
-            var validated = event.data.handler.logFoldChangeMaxValueInputValidation($(this).val());
-            event.data.handler.updateLogFoldChangeMaxValue(validated);
-        });
-
-        $(TOP_DATASET_SELECTION_SIDEBAR).on("change", {handler: this}, function (event) {
-            var selection = $(TOP_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value");
-            event.data.handler.updateTopDataset(selection);
-        });
-
-        $(BOTTOM_DATASET_SELECTION_SIDEBAR).on("change", {handler: this}, function (event) {
-            var selection = $(BOTTOM_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value");
-            event.data.handler.updateBottomDataset(selection);
-        });
-
-        $("#topDatasetDropdownMenu").on("click", "li", {handler: this}, function (event) {
-            event.data.handler.updateTopDataset($(this).attr("value"));
-        });
-
-        $("#bottomDatasetDropdownMenu").on("click", "li", {handler: this}, function (event) {
-            event.data.handler.updateBottomDataset($(this).attr("value"));
-        });
-    },
-
-    initialize: function () {
-        $(NODE_COLORING_TOGGLE_SIDEBAR).val("Enable Node Coloring");
-        $(AVG_REPLICATE_VALS_TOP_SIDEBAR).prop("checked", true);
-        $(AVG_REPLICATE_VALS_BOTTOM_SIDEBAR).prop("checked", true);
-        $(NODE_COLORING_TOGGLE_SIDEBAR).val("Disable Node Coloring");
-
-        // Initialize Menu Bar
-        $(AVG_REPLICATE_VALS_TOP_MENU + " span").addClass("glyphicon-ok");
-        $(AVG_REPLICATE_VALS_TOP_MENU).prop("checked", true);
-
-        $(AVG_REPLICATE_VALS_BOTTOM_MENU + " span").addClass("glyphicon-ok");
-        $(AVG_REPLICATE_VALS_BOTTOM_MENU).prop("checked", true);
-
-        $(NODE_COLORING_TOGGLE_MENU + " span").removeClass("glyphicon-ok");
-        $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(DEFAULT_MAX_LOG_FOLD_CHANGE);
-
-        this.logFoldChangeMaxValue = DEFAULT_MAX_LOG_FOLD_CHANGE;
-        this.nodeColoringEnabled = true;
-        this.avgTopDataset = true;
-        this.avgBottomDataset = true;
-        this.topDataset = undefined;
-        this.bottomDataset = undefined;
-        this.lastDataset = null;
-        this.bottomDataSameAsTop = true;
-    },
-
-    resetDatasetDropdownMenus: function (network) {
-
-        var createHTMLforDataset = function (name) {
-            return `
-            <li class=\"dataset-option node-coloring-menu\" value=\"${name}\">
-              <a>
-                <span class=\"glyphicon\"></span>
-                &nbsp;${name}
-              </a>
-            </li>`;
-        };
-
-        var nodeColoringOptions = [];
-        for (var property in network.expression) {
-            if (property.match(endsInExpressionRegExp)) {
-                nodeColoringOptions.push({value: property});
-            }
-        }
-        $(BOTTOM_DATASET_SELECTION_SIDEBAR).empty();
-        $(TOP_DATASET_SELECTION_SIDEBAR).empty();
-
-        $(".dataset-option").remove(); // clear all menu dataset options
-
-        $(BOTTOM_DATASET_SELECTION_SIDEBAR).append($("<option>")
-            .attr("value", "Same as Top Dataset").text("Same as Top Dataset"));
-
-        $(BOTTOM_DATASET_SELECTION_MENU).append(createHTMLforDataset("Same as Top Dataset"));
-
-        nodeColoringOptions.forEach(function (option) {
-            var shortenedSheetName = shortenExpressionSheetName(option.value);
-            $(TOP_DATASET_SELECTION_SIDEBAR).append($("<option>")
-              .attr("value", option.value).text(shortenedSheetName));
-            $(TOP_DATASET_SELECTION_MENU)
-              .append(createHTMLforDataset(option.value));
-            $(BOTTOM_DATASET_SELECTION_SIDEBAR).append($("<option>")
-              .attr("value", option.value).text(shortenedSheetName));
-            $(BOTTOM_DATASET_SELECTION_MENU)
-              .append(createHTMLforDataset(option.value));
-        });
-
-        $("#topDatasetDropdownMenu li a span").first().addClass("glyphicon-ok");
-        $("#bottomDatasetDropdownMenu li a span").first().addClass("glyphicon-ok");
-    },
-
-    isNewWorkbook: function (name) {
-        return this.lastDataset === null || this.lastDataset !== name;
-    },
-
-    showNodeColoringMenus: function () {
-        if ($(NODE_COLORING_MENU).hasClass("hidden")) {
-            $(NODE_COLORING_MENU).removeClass("hidden");
-        }
-        if ($(".node-coloring-menu").hasClass("disabled")) {
-            $(".node-coloring-menu").removeClass("disabled");
-        }
-    },
-
-    disableNodeColoringMenus: function () {
-        if (!$(NODE_COLORING_MENU).hasClass("hidden")) {
-            $(NODE_COLORING_MENU).addClass("hidden");
-        }
-        if (!$(".node-coloring-menu").hasClass("disabled")) {
-            $(".node-coloring-menu").addClass("disabled");
-        }
-    },
-
-    reload: function (network, name) {
-        if (hasExpressionData(network.expression)) {
-            this.showNodeColoringMenus();
-            if (this.isNewWorkbook(name)) {
-                this.initialize();
-                this.lastDataset = name;
-                this.resetDatasetDropdownMenus(network);
-            }
-            this.topDataset = $(TOP_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value");
-            if ($(BOTTOM_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value") === "Same as Top Dataset") {
-                this.bottomDataset = this.topDataset;
-                this.bottomDataSameAsTop = true;
-            } else {
-                this.bottomDataset = $(BOTTOM_DATASET_SELECTION_SIDEBAR).find(":selected").attr("value");
-                this.bottomDataSameAsTop = false;
-            }
-        } else {
-            this.disableNodeColoringMenus();
-        }
-    },
-};