grnsight/test/export-tests.js

Web app and service for visualizing models of gene regulatory networks

var expect = require("chai").expect;
var extend = require("jquery-extend");
var xlsx = require("node-xlsx");
var test = require("./test");
const { CELL_A1_PPI, CELL_A1_GRN } = require("../server/controllers/constants");

var exportController = require(__dirname + "/../server/controllers/export-controller")();
var constants = require(__dirname + "/../server/controllers/constants");

var unweightedTestWorkbook = {
    genes: [
        { name: "A" },
        { name: "B" },
        { name: "C" },
        { name: "D" }
    ],
    links: [
        { source: 2, target: 1 },
        { source: 1, target: 0 },
        { source: 1, target: 2 }
    ],
    errors: [],
    warnings: [],
    sheetType: "unweighted",
    workbookType: constants.NETWORK_GRN_MODE
};

var weightedTestWorkbook = {
    genes: [
        { name: "A" },
        { name: "B" },
        { name: "C" },
        { name: "D" }
    ],
    links: [
        { source: 2, target: 1, value: 0.5 },
        { source: 1, target: 0, value: -0.75 },
        { source: 1, target: 2, value: 0.25 }
    ],
    errors: [],
    warnings: [],
    sheetType: "weighted",
    workbookType: constants.NETWORK_GRN_MODE
};

var unweightedTestWorkbookWithCycle = {
    genes: [
        { name: "A" },
        { name: "B" },
        { name: "C" },
        { name: "D" },
        { name: "E" }
    ],
    links: [
        { source: 2, target: 1 },
        { source: 1, target: 0 },
        { source: 1, target: 2 },
        { source: 3, target: 3 },
        { source: 0, target: 0 }
    ],
    errors: [],
    warnings: [],
    sheetType: "unweighted",
    workbookType: "constants.NETWORK_GRN_MODE"
};

var weightedTestWorkbookWithCycle = {
    genes: [
        { name: "A" },
        { name: "B" },
        { name: "C" },
        { name: "D" },
        { name: "E" }
    ],
    links: [
        { source: 2, target: 1, value: 0.5 },
        { source: 1, target: 0, value: -0.75 },
        { source: 1, target: 2, value: 0.25 },
        { source: 3, target: 3, value: -0.375 },
        { source: 0, target: 0, value: 0.875 }
    ],
    errors: [],
    warnings: [],
    sheetType: "weighted",
    workbookType: constants.NETWORK_GRN_MODE
};

describe("Export to SIF", function () {
    it("should export unweighted workbooks to SIF correctly", function () {
        var lines = exportController.grnsightToSif(unweightedTestWorkbook).split("\n");
        expect(lines[0].split("\t")).to.deep.equal([ "A", "", "" ]);
        expect(lines[1].split("\t")).to.deep.equal([ "B", "pd", "A" ]);
        expect(lines[2].split("\t")).to.deep.equal([ "B", "pd", "C" ]);
        expect(lines[3].split("\t")).to.deep.equal([ "C", "pd", "B" ]);
        expect(lines[4].split("\t")).to.deep.equal([ "D", "", "" ]);
    });

    it("should export weighted workbooks to SIF correctly", function () {
        var lines = exportController.grnsightToSif(weightedTestWorkbook).split("\n");
        expect(lines[0].split("\t")).to.deep.equal([ "A", "", "" ]);
        expect(lines[1].split("\t")).to.deep.equal([ "B", "-0.75", "A" ]);
        expect(lines[2].split("\t")).to.deep.equal([ "B", "0.25", "C" ]);
        expect(lines[3].split("\t")).to.deep.equal([ "C", "0.5", "B" ]);
        expect(lines[4].split("\t")).to.deep.equal([ "D", "", "" ]);
    });

    it("should export unweighted workbooks with cycles to SIF correctly", function () {
        var lines = exportController.grnsightToSif(unweightedTestWorkbookWithCycle).split("\n");
        expect(lines[0].split("\t")).to.deep.equal([ "A", "pd", "A" ]);
        expect(lines[1].split("\t")).to.deep.equal([ "B", "pd", "A" ]);
        expect(lines[2].split("\t")).to.deep.equal([ "B", "pd", "C" ]);
        expect(lines[3].split("\t")).to.deep.equal([ "C", "pd", "B" ]);
        expect(lines[4].split("\t")).to.deep.equal([ "D", "pd", "D" ]);
        expect(lines[5].split("\t")).to.deep.equal([ "E", "", "" ]);
    });

    it("should export weighted workbooks with cycles to SIF correctly", function () {
        var lines = exportController.grnsightToSif(weightedTestWorkbookWithCycle).split("\n");
        expect(lines[0].split("\t")).to.deep.equal([ "A", "0.875", "A" ]);
        expect(lines[1].split("\t")).to.deep.equal([ "B", "-0.75", "A" ]);
        expect(lines[2].split("\t")).to.deep.equal([ "B", "0.25", "C" ]);
        expect(lines[3].split("\t")).to.deep.equal([ "C", "0.5", "B" ]);
        expect(lines[4].split("\t")).to.deep.equal([ "D", "-0.375", "D" ]);
        expect(lines[5].split("\t")).to.deep.equal([ "E", "", "" ]);
    });
});

var EXPORT_COMMENT = "<!-- Exported by GRNsight v" + constants.VERSION + "  " +
  "http://dondi.github.io/GRNsight/  " +
  "https://github.com/dondi/GRNsight/releases/tag/v" + constants.VERSION + " -->";

/* eslint-disable quotes */
// We'll allow single quotes here because graphMl has a lot of double quotes in it
// and it's easier to not escape them all.
describe("Export to GraphML", function () {
    it("should export unweighted workbooks to GraphML correctly", function () {
        var lines = exportController.grnsightToGraphMl(unweightedTestWorkbook).split("\n").map(function (line) {
            return line.trim();
        });

        var expectedGraphMlLines = [
            '<?xml version="1.0" encoding="UTF-8"?>',
            '<graphml xmlns="http://graphml.graphdrawing.org/xmlns" ' +
              'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' +
              'xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns ' +
              'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">',
            EXPORT_COMMENT,
            '<key id="name" for="node" attr.name="name" attr.type="string"/>',
            '<key id="interaction" for="edge" attr.name="interaction" attr.type="string"/>',
            '<key id="name" for="edge" attr.name="name" attr.type="string"/>',
            '<graph edgedefault="directed">',
            '<node id="A">',
            '<data key="name">A</data>',
            '</node>',
            '<node id="B">',
            '<data key="name">B</data>',
            '</node>',
            '<node id="C">',
            '<data key="name">C</data>',
            '</node>',
            '<node id="D">',
            '<data key="name">D</data>',
            '</node>',
            '<edge source="C" target="B">',
            '<data key="interaction">pd</data>',
            '<data key="name">C (pd) B</data>',
            '</edge>',
            '<edge source="B" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) A</data>',
            '</edge>',
            '<edge source="B" target="C">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) C</data>',
            '</edge>',
            '</graph>',
            '</graphml>'
        ];

        lines.forEach(function (line, index) {
            expect(line).to.equal(expectedGraphMlLines[index]);
        });
    });

    it("should export weighted workbooks to GraphML correctly", function () {
        var lines = exportController.grnsightToGraphMl(weightedTestWorkbook).split("\n").map(function (line) {
            return line.trim();
        });

        var expectedGraphMlLines = [
            '<?xml version="1.0" encoding="UTF-8"?>',
            '<graphml xmlns="http://graphml.graphdrawing.org/xmlns" ' +
              'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' +
              'xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns ' +
              'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">',
            EXPORT_COMMENT,
            '<key id="name" for="node" attr.name="name" attr.type="string"/>',
            '<key id="interaction" for="edge" attr.name="interaction" attr.type="string"/>',
            '<key id="name" for="edge" attr.name="name" attr.type="string"/>',
            '<key id="weight" for="edge" attr.name="weight" attr.type="double"/>',
            '<graph edgedefault="directed">',
            '<node id="A">',
            '<data key="name">A</data>',
            '</node>',
            '<node id="B">',
            '<data key="name">B</data>',
            '</node>',
            '<node id="C">',
            '<data key="name">C</data>',
            '</node>',
            '<node id="D">',
            '<data key="name">D</data>',
            '</node>',
            '<edge source="C" target="B">',
            '<data key="interaction">pd</data>',
            '<data key="name">C (pd) B</data>',
            '<data key="weight">0.5</data>',
            '</edge>',
            '<edge source="B" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) A</data>',
            '<data key="weight">-0.75</data>',
            '</edge>',
            '<edge source="B" target="C">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) C</data>',
            '<data key="weight">0.25</data>',
            '</edge>',
            '</graph>',
            '</graphml>'
        ];

        lines.forEach(function (line, index) {
            expect(line).to.equal(expectedGraphMlLines[index]);
        });
    });

    it("should export unweighted workbooks with cycles to GraphML correctly", function () {
        var lines = exportController.grnsightToGraphMl(unweightedTestWorkbookWithCycle).split("\n")
        .map(function (line) {
            return line.trim();
        });

        var expectedGraphMlLines = [
            '<?xml version="1.0" encoding="UTF-8"?>',
            '<graphml xmlns="http://graphml.graphdrawing.org/xmlns" ' +
              'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' +
              'xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns ' +
              'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">',
            EXPORT_COMMENT,
            '<key id="name" for="node" attr.name="name" attr.type="string"/>',
            '<key id="interaction" for="edge" attr.name="interaction" attr.type="string"/>',
            '<key id="name" for="edge" attr.name="name" attr.type="string"/>',
            '<graph edgedefault="directed">',
            '<node id="A">',
            '<data key="name">A</data>',
            '</node>',
            '<node id="B">',
            '<data key="name">B</data>',
            '</node>',
            '<node id="C">',
            '<data key="name">C</data>',
            '</node>',
            '<node id="D">',
            '<data key="name">D</data>',
            '</node>',
            '<node id="E">',
            '<data key="name">E</data>',
            '</node>',
            '<edge source="C" target="B">',
            '<data key="interaction">pd</data>',
            '<data key="name">C (pd) B</data>',
            '</edge>',
            '<edge source="B" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) A</data>',
            '</edge>',
            '<edge source="B" target="C">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) C</data>',
            '</edge>',
            '<edge source="D" target="D">',
            '<data key="interaction">pd</data>',
            '<data key="name">D (pd) D</data>',
            '</edge>',
            '<edge source="A" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">A (pd) A</data>',
            '</edge>',
            '</graph>',
            '</graphml>'
        ];

        lines.forEach(function (line, index) {
            expect(line).to.equal(expectedGraphMlLines[index]);
        });
    });

    it("should export weighted workbooks with cycles to GraphML correctly", function () {
        var lines = exportController.grnsightToGraphMl(weightedTestWorkbookWithCycle).split("\n").map(function (line) {
            return line.trim();
        });

        var expectedGraphMlLines = [
            '<?xml version="1.0" encoding="UTF-8"?>',
            '<graphml xmlns="http://graphml.graphdrawing.org/xmlns" ' +
              'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' +
              'xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns ' +
              'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">',
            EXPORT_COMMENT,
            '<key id="name" for="node" attr.name="name" attr.type="string"/>',
            '<key id="interaction" for="edge" attr.name="interaction" attr.type="string"/>',
            '<key id="name" for="edge" attr.name="name" attr.type="string"/>',
            '<key id="weight" for="edge" attr.name="weight" attr.type="double"/>',
            '<graph edgedefault="directed">',
            '<node id="A">',
            '<data key="name">A</data>',
            '</node>',
            '<node id="B">',
            '<data key="name">B</data>',
            '</node>',
            '<node id="C">',
            '<data key="name">C</data>',
            '</node>',
            '<node id="D">',
            '<data key="name">D</data>',
            '</node>',
            '<node id="E">',
            '<data key="name">E</data>',
            '</node>',
            '<edge source="C" target="B">',
            '<data key="interaction">pd</data>',
            '<data key="name">C (pd) B</data>',
            '<data key="weight">0.5</data>',
            '</edge>',
            '<edge source="B" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) A</data>',
            '<data key="weight">-0.75</data>',
            '</edge>',
            '<edge source="B" target="C">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) C</data>',
            '<data key="weight">0.25</data>',
            '</edge>',
            '<edge source="D" target="D">',
            '<data key="interaction">pd</data>',
            '<data key="name">D (pd) D</data>',
            '<data key="weight">-0.375</data>',
            '</edge>',
            '<edge source="A" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">A (pd) A</data>',
            '<data key="weight">0.875</data>',
            '</edge>',
            '</graph>',
            '</graphml>'
        ];

        lines.forEach(function (line, index) {
            expect(line).to.equal(expectedGraphMlLines[index]);
        });
    });

    it("should export workbooks with a filename as the graph element id", function () {
        var workbookWithFilename = extend(true, unweightedTestWorkbook, { filename: "hello.graphml" });
        var lines = exportController.grnsightToGraphMl(workbookWithFilename).split("\n").map(function (line) {
            return line.trim();
        });
        var expectedGraphMlLines = [
            '<?xml version="1.0" encoding="UTF-8"?>',
            '<graphml xmlns="http://graphml.graphdrawing.org/xmlns" ' +
              'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' +
              'xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns ' +
              'http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">',
            EXPORT_COMMENT,
            '<key id="name" for="node" attr.name="name" attr.type="string"/>',
            '<key id="interaction" for="edge" attr.name="interaction" attr.type="string"/>',
            '<key id="name" for="edge" attr.name="name" attr.type="string"/>',
            '<graph edgedefault="directed" id="hello.graphml">',
            '<node id="A">',
            '<data key="name">A</data>',
            '</node>',
            '<node id="B">',
            '<data key="name">B</data>',
            '</node>',
            '<node id="C">',
            '<data key="name">C</data>',
            '</node>',
            '<node id="D">',
            '<data key="name">D</data>',
            '</node>',
            '<edge source="C" target="B">',
            '<data key="interaction">pd</data>',
            '<data key="name">C (pd) B</data>',
            '</edge>',
            '<edge source="B" target="A">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) A</data>',
            '</edge>',
            '<edge source="B" target="C">',
            '<data key="interaction">pd</data>',
            '<data key="name">B (pd) C</data>',
            '</edge>',
            '</graph>',
            '</graphml>'
        ];

        lines.forEach(function (line, index) {
            expect(line).to.equal(expectedGraphMlLines[index]);
        });
    });
});

const inputPPIWorkbook = {
    "genes": [
        { "name": "Aim32p" },
        { "name": "Ccr4p" },
        { "name": "Erv1p" }
    ],

    "links": [
        {
            "source": 0,
            "target": 1,
            "value": 1,
            "type": "arrowhead",
            "stroke": "black"
        },
        {
            "source": 1,
            "target": 1,
            "value": 1,
            "type": "arrowhead",
            "stroke": "black",
        },
        {
            "source": 0,
            "target": 2,
            "value": 1,
            "type": "arrowhead",
            "stroke": "black",
        },
        {
            "source": 2,
            "target": 2,
            "value": 1,
            "type": "arrowhead",
            "stroke": "black",
        }
    ],

    network: {
        "genes": [
            { "name": "Aim32p" },
            { "name": "Ccr4p" },
            { "name": "Erv1p" }
        ],

        "links": [
            {
                "source": 0,
                "target": 1,
                "value": 1,
                "type": "arrowhead",
                "stroke": "black"
            },
            {
                "source": 1,
                "target": 1,
                "value": 1,
                "type": "arrowhead",
                "stroke": "black",
            },
            {
                "source": 0,
                "target": 2,
                "value": 1,
                "type": "arrowhead",
                "stroke": "black",
            },
            {
                "source": 2,
                "target": 2,
                "value": 1,
                "type": "arrowhead",
                "stroke": "black",
            }
        ],
    },
    networkWeights: {},

    "meta": {
        data: {
            "workbookType": "protein-protein-physical-interaction",
            "species": "Saccharomyces cerevisiae",
            "taxon_id": "559292",
        }
    },
};

inputPPIWorkbook.exportSheets = {
    networks: {
        "network": inputPPIWorkbook.network
    },
    "optimization_parameters": inputPPIWorkbook.meta
};

const inputWorkbook = {
    "genes": [
        { "name": "ACE2" },
        { "name": "AFT2" },
        { "name": "CIN5" },
    ],

    "links": [
        {
            "source": 0,
            "target": 0,
            "value": 1,
            type: "arrowhead",
            stroke: "black"
        },

        {
            source: 1,
            target: 1,
            value: 1,
            type: "arrowhead",
            stroke: "black"
        },

        {
            source: 2,
            target: 1,
            value: 1,
            type: "arrowhead",
            stroke: "black"
        },

        {
            source: 2,
            target: 2,
            value: 1,
            type: "arrowhead",
            stroke: "black"
        }
    ],

    network: {
        "genes": [
            { "name": "ACE2" },
            { "name": "AFT2" },
            { "name": "CIN5" },
        ],

        "links": [
            {
                "source": 0,
                "target": 0,
                "value": 1,
                type: "arrowhead",
                stroke: "black"
            },

            {
                source: 1,
                target: 1,
                value: 1,
                type: "arrowhead",
                stroke: "black"
            },

            {
                source: 2,
                target: 1,
                value: 1,
                type: "arrowhead",
                stroke: "black"
            },

            {
                source: 2,
                target: 2,
                value: 1,
                type: "arrowhead",
                stroke: "black"
            }
        ],
    },

    networkWeights: {
        "genes": [
            { "name": "ACE2" },
            { "name": "AFT2" },
            { "name": "CIN5" },
        ],

        "links": [
            {
                "source": 0,
                "target": 0,
                "value": 1,
                type: "arrowhead",
                stroke: "black"
            },

            {
                source: 1,
                target: 1,
                value: 1,
                type: "arrowhead",
                stroke: "black"
            },

            {
                source: 2,
                target: 1,
                value: 1,
                type: "arrowhead",
                stroke: "black"
            },

            {
                source: 2,
                target: 2,
                value: 1,
                type: "arrowhead",
                stroke: "black"
            }
        ],
    },

    "meta": {
        data: {
            "L_curve": 0,
            "MaxFunEval": 1000000,
            "MaxIter": 1000000,
            "Strain": ["wt", "dcin5"],
            "TolFun": 0.00001,
            "TolX": 0.00001,
            "alpha": 0.001,
            "estimate_params": 1,
            "expression_timepoints": [0.4, 0.8, 1.2],
            "fix_P": 1,
            "fix_b": 0,
            "kk_max": 1,
            "make_graphs": 1,
            "production_function": "testMM",
            "simulation_timepoints": [0, 0.1, 0.2],
            "species": "Saccharomyces cerevisiae",
            "taxon_id": 559292,
            "workbookType": constants.NETWORK_GRN_MODE
        }
    },

    "test": {
        "production_rates": {
            data: {
                "ACE2": 0.5,
                "AFT2": 1,
                "CIN5": 2
            }
        },

        "degradation_rates": {
            data: {
                "ACE2": 1,
                "AFT2": 1,
                "CIN5": 1
            }
        },

        "threshold_b": {
            data: {
                "ACE2": 0,
                "AFT2": 0,
                "CIN5": 0
            }
        }
    },


    "exportExpression": {
        "wt_log2_expression": {
            "timePoints": [
                0.4,
                0.8,
                1.2
            ],
            "data": {
                "id": [
                    0.4,
                    0.8,
                    1.2
                ],
                "ACE2": [
                    1,
                    2,
                    3
                ],

                "AFT2": [
                    4,
                    5,
                    6
                ],

                "CIN5": [
                    7,
                    8,
                    9
                ]
            }
        },

        "dcin5_log2_expression": {
            "timePoints": [
                0.4,
                0.8,
                1.2
            ],
            "data": {
                "id": [
                    0.4,
                    0.8,
                    1.2
                ],
                "ACE2": [
                    10,
                    11,
                    12
                ],

                "AFT2": [
                    13,
                    14,
                    15
                ],

                "CIN5": [
                    16,
                    17,
                    18
                ]
            }
        }
    }
};

inputWorkbook.exportSheets = {
    networks: {
        "network": inputWorkbook.network,
        "network_weights": inputWorkbook.networkWeights
    },
    "optimization_parameters": inputWorkbook.meta,
    "two_column_sheets": inputWorkbook.test,
    expression: inputWorkbook.exportExpression
};

describe("Export to spreadsheet", function () {
    it("should export a workbook of gene regulatory network to a spreadsheet object properly", function () {
        const expectedSheet = [
            {
                name: "network",
                data: [
                    [CELL_A1_GRN, "ACE2", "AFT2", "CIN5"],
                    ["ACE2", 1, 0, 0],
                    ["AFT2", 0, 1, 1],
                    ["CIN5", 0, 0, 1]
                ]
            },

            {
                name: "network_weights",
                data: [
                    [CELL_A1_GRN, "ACE2", "AFT2", "CIN5"],
                    ["ACE2", 1, 0, 0],
                    ["AFT2", 0, 1, 1],
                    ["CIN5", 0, 0, 1]
                ]
            },

            {
                name: "optimization_parameters",
                data: [
                    ["optimization_parameter", "value"],
                    ["L_curve", 0],
                    ["MaxFunEval", 1000000],
                    ["MaxIter", 1000000],
                    ["Strain", "wt", "dcin5"],
                    ["TolFun", 0.00001],
                    ["TolX", 0.00001],
                    ["alpha", 0.001],
                    ["estimate_params", 1],
                    ["expression_timepoints", 0.4, 0.8, 1.2],
                    ["fix_P", 1],
                    ["fix_b", 0],
                    ["kk_max", 1],
                    ["make_graphs", 1],
                    ["production_function", "testMM"],
                    ["simulation_timepoints", 0, 0.1, 0.2],
                    ["species", "Saccharomyces cerevisiae"],
                    ["taxon_id", 559292],
                    ["workbookType", constants.NETWORK_GRN_MODE]
                ]
            },

            {
                name: "production_rates",
                data: [
                    ["id", "production_rate"],
                    ["ACE2", 0.5],
                    ["AFT2", 1],
                    ["CIN5", 2],
                ]
            },

            {
                name: "degradation_rates",
                data: [
                    ["id", "degradation_rate"],
                    ["ACE2", 1],
                    ["AFT2", 1],
                    ["CIN5", 1]
                ]
            },

            {
                name: "threshold_b",
                data: [
                    ["id", "threshold_b"],
                    ["ACE2", 0],
                    ["AFT2", 0],
                    ["CIN5", 0]
                ]
            },

            {
                name: "wt_log2_expression",
                data:
                [
                    ["id", 0.4, 0.8, 1.2],
                    [
                        "ACE2",
                        1,
                        2,
                        3
                    ],
                    [
                        "AFT2",
                        4,
                        5,
                        6
                    ],
                    [
                        "CIN5",
                        7,
                        8,
                        9
                    ]
                ]
            },

            {
                name: "dcin5_log2_expression",
                data: [
                    ["id", 0.4, 0.8, 1.2],
                    [
                        "ACE2",
                        10,
                        11,
                        12
                    ],
                    [
                        "AFT2",
                        13,
                        14,
                        15
                    ],
                    [
                        "CIN5",
                        16,
                        17,
                        18
                    ]
                ]
            }
        ];

        const actualSheet = exportController.grnsightToXlsx(inputWorkbook);
        expect(actualSheet).to.deep.equal(xlsx.build(expectedSheet));
    });

    it("should export a workbook of ppi to a spreadsheet object properly", function () {
        const expectedSheet = [
            {
                name: "network",
                data: [
                    [CELL_A1_PPI, "Aim32p", "Ccr4p", "Erv1p"],
                    ["Aim32p", 0, 0, 0],
                    ["Ccr4p", 1, 1, 0],
                    ["Erv1p", 1, 0, 1]
                ]
            },

            {
                name: "optimization_parameters",
                data: [
                    ["optimization_parameter", "value"],
                    ["workbookType", constants.NETWORK_PPI_MODE],
                    ["species", "Saccharomyces cerevisiae"],
                    ["taxon_id", "559292"]
                ]
            }
        ];
        const actualSheet = exportController.grnsightToXlsx(inputPPIWorkbook);
        expect(actualSheet).to.deep.equal(xlsx.build(expectedSheet));
    });

    it("should export a workbook exactly as the import",
        function () {
            // Commented out temporarily while reworking the export of the optimization diagnostics sheet
            // test.importFileSameAsExportFile(
            //     "test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx");
            test.importFileSameAsExportFile(
                "test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx");
            test.importFileSameAsExportFile(
                "test-files/additional-sheet-test-files/optimization-parameters-default.xlsx");
        }
    );

    it("should import a workbook with minor additional sheet warnings," +
    " export the workbook, and import the exported workbook properly",
        function () {
            test.importExportReImportNoErrorsOrWarnings(
                "test-files/additional-sheet-test-files/optimization-parameters-incorrect-headers.xlsx");
            test.importExportReImportNoErrorsOrWarnings(
                "test-files/additional-sheet-test-files/two-column-sheets-missing-column-header.xlsx");
            test.importExportReImportNoErrorsOrWarnings(
                "test-files/additional-sheet-test-files/optimization-diagnostics-incorrect-MSE-gene-header.xlsx");
        }
    );

    it("should import a workbook with no warnings, export the workbook, and import the exported workbook properly",
        function () {
            test.importExportReImportNoErrorsOrWarnings(
                "test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx");
        }
    );
});