grnsight 4.0.0 → 6.0.0

package/onlysidebar.html

@@ -1,8 +0,0 @@
-<div id="stickyBar" data-spy="affix" data-offset-top="140">
-    <ul class="nav">
-{% include menu.html %}
-    </ul>
-    <p id="modText" class="modNav">
-        Last modified: {{ page.modified }}
-    </p>
-</div>

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});
-        }
-    });
-
-};