grnsight 5.1.0 → 6.0.4

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

@@ -5,12 +5,31 @@
 /* eslint-disable max-len */
 import { grnState } from "./grnstate";
 
+
 import {
-    buildURL,
-    responseData,
-    stopLoadingIcon
+    stopLoadingIcon,
+    startLoadingIcon
 } from "./update-app";
 
+import { queryExpressionDatabase } from "./api/grnsight-api.js";
+
+
+const EXPRESSION_SHEET_SUFFIXES = ["_expression", "_optimized_expression", "_sigmas"];
+
+const isExpressionSheet = (sheetName) => {
+    return EXPRESSION_SHEET_SUFFIXES.some(function (suffix) {
+        return sheetName.includes(suffix);
+    });
+};
+
+const removeExpressionSuffix = (sheetName) => {
+    let sheet = sheetName.split("_log2").join("").split("_log").join("");
+    for (let suffix of EXPRESSION_SHEET_SUFFIXES) {
+        sheet = sheet.split(suffix).join("");
+    }
+    return sheet;
+};
+
 export const uploadState = {
     currentWorkbook: null,
 };
@@ -72,16 +91,139 @@ export const upload = function () {
         return filename + "." + extension;
     };
 
+    const exportExcel = (route, extension, sheetType) => {
+        if (!$(this).parent().hasClass("disabled")) {
+            var workbookToExport = flattenWorkbook(uploadState.currentWorkbook, sheetType);
+            var workbookFilename = filenameWithExtension(sheetType !== uploadState.currentWorkbook.sheetType ?
+                sheetType : "", extension);
+            workbookToExport.filename = workbookFilename;
+            var exportForm = $("<form></form>").attr({
+                method: "POST",
+                action: $(".service-root").val() + "/" + route
+            }).append($("<input></input>").attr({
+                type: "hidden",
+                name: "filename",
+                value: workbookFilename
+            })).append($("<input></input>").attr({
+                type: "hidden",
+                name: "workbook",
+                value: JSON.stringify(workbookToExport)
+            }));
+            $("body").append(exportForm);
+            exportForm.submit();
+            exportForm.remove();
+        }
+        $("#exportExcelModal").modal("hide");
+    };
+
+    const updateOptimizationParameters =  (finalExportSheets) => {
+        let optimizationParameters = {
+            data: {
+                alpha: 0.002,
+                "kk_max": 1,
+                MaxIter: 100000000,
+                TolFun: 0.000001,
+                MaxFunEval: 100000000,
+                TolX: 0.000001,
+                "production_function": "Sigmoid",
+                "L_curve": 0,
+                "estimate_params": 1,
+                "make_graphs": 1,
+                "fix_P": 0,
+                "fix_b": 0,
+            }
+        };
+        const expression = Object.keys(finalExportSheets.expression);
+        let expTimepoints = expression.length > 0 ? finalExportSheets.expression[expression[0]].timePoints : null;
+        expTimepoints = expTimepoints ? [...(new Set(expTimepoints))].sort(function (a, b) {
+            return a - b;
+        }) : null;
+        const simTimepoints = expTimepoints ? Array.from(Array(expTimepoints[expTimepoints.length - 1] + 1).keys()).filter(x => x % 5 === 0) : null;
+        const strain = expression.length > 0 ? expression.map(x => removeExpressionSuffix(x)) : null;
+        if (expTimepoints) {
+            optimizationParameters.data["expression_timepoints"] = expTimepoints;
+        }
+        if (strain) {
+            optimizationParameters.data.Strain = strain;
+        }
+        if (simTimepoints) {
+            optimizationParameters.data["simulation_timepoints"] = simTimepoints;
+        }
+        optimizationParameters.data.species = "Saccharomyces cerevisiae";
+        optimizationParameters.data["taxon_id"] = 559292;
+        return optimizationParameters;
+    };
+
+    const handleExpressionDataAndExport = (route, extension, sheetType, source, finalExportSheets) => {
+        if (source === "userInput" && grnState.workbook.expression) {
+            // make sure that the optimization parameters sheet is actually properly formatted
+            if (finalExportSheets["optimization_parameters"]) {
+                finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets);
+            }
+            grnState.workbook.exportSheets = finalExportSheets;
+            exportExcel(route, extension, sheetType);
+        } else {
+            // expression source is from database so lets query her up
+            for (let sheet in finalExportSheets.expression) {
+                startLoadingIcon();
+                const dataset = `${source}_${sheet.replace("_log2_expression", "")}`;
+                queryExpressionDatabase({
+                    type: "ExpressionTimePoints",
+                    dataset
+                }).then(function (timepointsResponse) {
+                    queryExpressionDatabase({
+                        type:"ExpressionData",
+                        dataset,
+                        genes : grnState.workbook.genes.map(x => {
+                            return x.name;
+                        }).join(","),
+                        timepoints: timepointsResponse[dataset]
+                    }).then(function (response) {
+                        finalExportSheets.expression[sheet] = response;
+                        if (finalExportSheets.expression[sheet]) {
+                            stopLoadingIcon();
+                            if ( !Object.values(finalExportSheets.expression).includes(null) ) {
+                                // we have all of the expression sheets so lets initilize the export process
+                                Object.keys(finalExportSheets.expression).forEach((sheet) => {
+                                    // make sure that the sheets we queried are populated with the correct data
+                                    if (!(finalExportSheets.expression[sheet].data && finalExportSheets.expression[sheet].timePoints)) {
+                                        // if the resulting query doesn't contains both the timePoint data and
+                                        // the gene data then don't export it. If not don't :)
+                                        finalExportSheets.expression[sheet] = null;
+                                    }
+                                });
+                                if (finalExportSheets["optimization_parameters"] === null) {
+                                    finalExportSheets["optimization_parameters"] = updateOptimizationParameters(finalExportSheets);
+                                }
+                                grnState.workbook.exportSheets = finalExportSheets;
+                                exportExcel(route, extension, sheetType);
+                            }
+                        }
+                    }).catch(function (error) {
+                        console.log(error.stack);
+                        console.log(error.name);
+                        console.log(error.message);
+                    });
+                }).catch(function (error) {
+                    console.log(error.stack);
+                    console.log(error.name);
+                    console.log(error.message);
+                });
+            }
+        }
+    };
+
+
     const handleExportExcelButtonExport = (route, extension, sheetType, source) => {
         grnState.workbook.exportNetworkType = sheetType;
-        const expressionSheets = $("input[name=expressionSheets]:checked");
+        const workbookSheets = $("input[name=workbookSheets]:checked");
         var chosenSheets = [];
-        for (const [key, value] of Object.entries(expressionSheets)) {
+        for (const [key, value] of Object.entries(workbookSheets)) {
             if (!isNaN(parseInt(key, 10))) {
                 if (value.value === "select all") {
-                    const allExpressionSheets = $("input[name=expressionSheets]");
+                    const allWorkbookSheets = $("input[name=workbookSheets]");
                     chosenSheets = [];
-                    for (const [k, v] of Object.entries(allExpressionSheets)) {
+                    for (const [k, v] of Object.entries(allWorkbookSheets)) {
                         if (!isNaN(parseInt(k, 10))) {
                             if (v.value !== "select all") {
                                 chosenSheets.push(v.value);
@@ -94,90 +236,88 @@ export const upload = function () {
                 }
             }
         }
-        const exportSheets = {};
-
-        if (source === "userInput" && grnState.workbook.expression) {
-            // source is from user speadsheet
-            // parse through grnState expression sheets and collect the sheets to be exported
-            for (let sheet of chosenSheets) {
-                if (grnState.workbook.expression[sheet]) {
-                    exportSheets[sheet] = grnState.workbook.expression[sheet];
+        const finalExportSheets = {
+            networks: {},
+            expression: {},
+            "two_column_sheets": {}
+        };
+        const twoColumnSheets = grnState.workbook.twoColumnSheets ? Object.keys(grnState.workbook.twoColumnSheets) : [];
+        // Collect all of the Sheets to be exported
+        for (let sheet of chosenSheets) {
+            if (sheet === "network_optimized_weights") {
+                finalExportSheets.networks[sheet] = grnState.workbook.networkOptimizedWeights;
+            } else if (sheet === "network") {
+                finalExportSheets.networks[sheet] = grnState.workbook.network;
+            } else if (sheet === "network_weights") {
+                finalExportSheets.networks[sheet] = grnState.workbook.networkWeights;
+            } else if (sheet === "optimization_diagnostics") { // Get the additional Sheets
+                finalExportSheets[sheet] = grnState.workbook.meta2;
+            } else if (sheet === "optimization_parameters") {
+                finalExportSheets[sheet] = source === "userInput" ? grnState.workbook.meta : null;
+            } else if (isExpressionSheet(sheet)) {
+                finalExportSheets.expression[sheet] = source === "userInput" ? grnState.workbook.expression[sheet] : null;
+            } else {
+                if (source === "userInput" && twoColumnSheets.indexOf(sheet) !== -1) {
+                    finalExportSheets.two_column_sheets[sheet] = grnState.workbook.twoColumnSheets[sheet];
+                } else {
+                    // Generate the two column sheet specified
+                    if (source === "userInput" && Object.keys(finalExportSheets.two_column_sheets).includes(sheet)) {
+                        finalExportSheets.two_column_sheets[sheet] = grnState.workbook.two_column_sheets[sheet];
+                    } else if (sheet === "threshold_b") {
+                        finalExportSheets.two_column_sheets[sheet] = {
+                            data: {},
+                            errors: [],
+                            warnings: []
+                        };
+                        for (let g of grnState.workbook.genes) {
+                            finalExportSheets.two_column_sheets[sheet].data[g.name] = 0;
+                        }
+                    } else {
+                        finalExportSheets.two_column_sheets[sheet] = null;
+                    }
                 }
             }
-            grnState.workbook.exportExpression = exportSheets;
-            if (!$(this).parent().hasClass("disabled")) {
-                var workbookToExport = flattenWorkbook(uploadState.currentWorkbook, sheetType);
-                var workbookFilename = filenameWithExtension(sheetType !== uploadState.currentWorkbook.sheetType ?
-                    sheetType : "", extension);
-                workbookToExport.filename = workbookFilename;
-
-                var exportForm = $("<form></form>").attr({
-                    method: "POST",
-                    action: $("#service-root").val() + "/" + route
-                }).append($("<input></input>").attr({
-                    type: "hidden",
-                    name: "filename",
-                    value: workbookFilename
-                })).append($("<input></input>").attr({
-                    type: "hidden",
-                    name: "workbook",
-                    value: JSON.stringify(workbookToExport)
-                }));
-                $("body").append(exportForm);
-                exportForm.submit();
-                exportForm.remove();
-            }
-            $("#exportExcelModal").modal("hide");
-        } else {
-            // source is from database so lets query her up
-            for (let sheet of chosenSheets) {
-                let queryURL = buildURL({ dataset: sheet });
-                responseData("", queryURL).then(function (response) {
-                    exportSheets[sheet] = response;
-                    if (exportSheets[sheet]) {
-                        stopLoadingIcon();
-                        if (Object.keys(exportSheets).length === chosenSheets.length) {
-                            // we have all of the sheets so lets initilize the export process
-                            const finalExportSheets = {};
-                            Object.keys(exportSheets).forEach((sheet) => {
-                                // make sure that the sheets we queried are populated with the correct data
-                                if (exportSheets[sheet].data && exportSheets[sheet].timePoints) {
-                                    // if the resulting query contains both the timePoint data and
-                                    // the gene data then export it. If not don't :)
-                                    finalExportSheets[sheet] = exportSheets[sheet];
-                                }
-                            });
-                            grnState.workbook.exportExpression = finalExportSheets;
-                            if (!$(this).parent().hasClass("disabled")) {
-                                var workbookToExport = flattenWorkbook(uploadState.currentWorkbook, sheetType);
-                                var workbookFilename = filenameWithExtension(sheetType !== uploadState.currentWorkbook.sheetType ?
-                                    sheetType : "", extension);
-                                workbookToExport.filename = workbookFilename;
-                                var exportForm = $("<form></form>").attr({
-                                    method: "POST",
-                                    action: $("#service-root").val() + "/" + route
-                                }).append($("<input></input>").attr({
-                                    type: "hidden",
-                                    name: "filename",
-                                    value: workbookFilename
-                                })).append($("<input></input>").attr({
-                                    type: "hidden",
-                                    name: "workbook",
-                                    value: JSON.stringify(workbookToExport)
-                                }));
-                                $("body").append(exportForm);
-                                exportForm.submit();
-                                exportForm.remove();
-                            }
-                            $("#exportExcelModal").modal("hide");
-                        }
+        }
+        const twoColumnSheetType = {"production_rates" : "ProductionRates", "degradation_rates":"DegradationRates" };
+        const twoColumnQuerySheets = Object.keys(finalExportSheets.two_column_sheets).filter( x => finalExportSheets.two_column_sheets[x] === null);
+        if (twoColumnQuerySheets.length > 0) {
+            // if we need to query production rates and degradation rates
+            for (let sheet of twoColumnQuerySheets) {
+                if (finalExportSheets.two_column_sheets[sheet] === null) {
+                    let result = {
+                        data: {},
+                        errors: [],
+                        warnings: []
+                    };
+                    let genes = [];
+                    for (let g of grnState.workbook.genes) {
+                        genes.push(g.name);
                     }
-                }).catch(function (error) {
-                    console.log(error.stack);
-                    console.log(error.name);
-                    console.log(error.message);
-                });
+
+                    queryExpressionDatabase({
+                        type:twoColumnSheetType[sheet],
+                        genes:grnState.workbook.genes.map(x => {
+                            return x.name;
+                        }).join(",")
+                    }).then(function (response) {
+                        result.data = response;
+                        finalExportSheets.two_column_sheets[sheet] = result;
+                        if (!Object.values(finalExportSheets.two_column_sheets).includes(null)) {
+                            // if we got all of the two column sheets, then proceed with export
+                            handleExpressionDataAndExport(route, extension, sheetType, source, finalExportSheets);
+                        }
+
+                    }).catch(function (error) {
+                        console.log(error.stack);
+                        console.log(error.name);
+                        console.log(error.message);
+                    });
+
+                }
             }
+        } else {
+            // you already have all of your two column sheet, so move through expressi5on
+            handleExpressionDataAndExport(route, extension, sheetType, source, finalExportSheets);
         }
     };
 
@@ -195,7 +335,7 @@ export const upload = function () {
 
                     var exportForm = $("<form></form>").attr({
                         method: "POST",
-                        action: $("#service-root").val() + "/" + route
+                        action: $(".service-root").val() + "/" + route
                     }).append($("<input></input>").attr({
                         type: "hidden",
                         name: "filename",
@@ -215,166 +355,148 @@ export const upload = function () {
     };
 
     const createHTMLforForm1 = () => {
-        return `
-            <form id=\'exportExcelForm1\'>
-                <div class=\'form-group\'>
-                    <p id=\'exportExcelNetwork\'></p>
-                    <ul class=\'export-radio-group\' id=\'export-excel-weights-list\' style=\"list-style-type:none;\"> </ul>
-                </div>
-                <div class=\'form-group\'>
-                    <p id=\'exportExcelExpressionSources\'> </p>
-                    <ul class=\'export-radio-group\' id=\'export-excel-expression-source-list\' style=\"list-style-type:none;\">
-                        <li>
-                            <input type=\'radio\' name=\'expressionSource\' checked=\"true\" value=\"userInput\" id=\'exportExcelExpressionSource-userInputRadio\' class=\'export-radio\' />
-                            <label for=\'exportExcelExpressionSource-userInputRadio\' id=\'exportExcelExpressionSource-userInput\' class=\'export-radio-label\'> </label>
-                        </li>
-                        <li>
-                            <input type=\'radio\' name=\'expressionSource\' value=\"Dahlquist_2018\" id=\'exportExcelExpressionSource-DahlquistRadio\' class=\'export-radio\' />
-                            <label for=\'exportExcelExpressionSource-DahlquistRadio\' id=\'exportExcelExpressionSource-Dahlquist\' class=\'export-radio-label\'>  </label>
-                        </li>
-                        <li>
-                            <input type=\'radio\' name=\'expressionSource\' value=\"Kitagawa_2002\" id=\'exportExcelExpressionSource-KitagawaRadio\' class=\'export-radio\' />
-                            <label for=\'exportExcelExpressionSource-KitagawaRadio\' id=\'exportExcelExpressionSource-Kitagawa\' class=\'export-radio-label\'> </label>
-                        </li>
-                        <li>
-                            <input type=\'radio\' name=\'expressionSource\' value=\"Thorsen_2007\" id=\'exportExcelExpressionSource-ThorsenRadio\' class=\'export-radio\' />
-                            <label for=\'exportExcelExpressionSource-ThorsenRadio\' id=\'exportExcelExpressionSource-Thorsen\' class=\'export-radio-label\'> </label>
-                        </li>
-                        <li>
-                            <input type=\'radio\' name=\'expressionSource\' value=\"Barreto_2012\" id=\'exportExcelExpressionSource-BarretoRadio\' class=\'export-radio\' />
-                            <label for=\'exportExcelExpressionSource-BarretoRadio\' id=\'exportExcelExpressionSource-Barreto\' class=\'export-radio-label\'> </label>
-                        </li>
-                    </ul>
-                </div>
-                <button type=\'submit\' class=\'btn btn-default\' id=\'exportExcelContinueButton\'> Continue </button>
-            </form>
-        `;
+        const sources = [...new Set(grnState.database.expressionDatasets.map(s => s.slice(0, s.lastIndexOf("_"))) )];
+        let result = `
+        <form id=\'exportExcelForm1\'>
+            <div class=\'form-group export-form-group\'>
+                <p id=\'exportExcelNetwork\'></p>
+                <ul class=\'export-radio-group\' id=\'export-excel-weights-list\' style=\"list-style-type:none;\"> </ul>
+            </div>
+            <div class=\'form-group export-form-group\'>
+                <p id=\'exportExcelExpressionSources\'> </p>
+                <ul class=\'export-radio-group\' id=\'export-excel-expression-source-list\' style=\"list-style-type:none;\">
+                    <li>
+                        <input type=\'radio\' name=\'expressionSource\' checked=\"true\" value=\"userInput\" id=\'exportExcelExpressionSource-userInputRadio\' class=\'export-radio\' />
+                        <label for=\'exportExcelExpressionSource-userInputRadio\' id=\'exportExcelExpressionSource-userInput\' class=\'export-radio-label\'> </label>
+                    </li>`;
+        for (let source of sources) {
+            result += `
+            <li>
+                <input type=\'radio\' name=\'expressionSource\' value=\"${source}\" id=\'exportExcelExpressionSource-${source}Radio\' class=\'export-radio\' />
+                <label for=\'exportExcelExpressionSource-${source}Radio\' id=\'exportExcelExpressionSource-${source}\' class=\'export-radio-label\'>${source}</label>
+            </li>`;
+        }
+
+        result += "</ul></div></form>";
+        return result;
     };
 
     const createHTMLforForm2 = () => {
         return `
         <form id=\'exportExcelForm2\'>
-            <div class=\'form-group\'>
-                <p id=\'exportExcelExpressionSheets\'></p>
-                <ul class=\'exportExcelExpressionSheets\' id=\'export-excel-expression-sheet-list\' style=\"list-style-type:none;\"> </ul>
+            <div class=\'form-group export-form-group\'>
+                <p id=\'exportExcelWorkbookSheets\'></p>
+                <ul class=\'exportExcelWorkbookSheets\' id=\'export-excel-workbook-sheet-list\' style=\"list-style-type:none;\"> </ul>
             </div>
-            <input type=\'button\' class=\'btn btn-default\' id=\'exportExcelButton\' value=\'Export Workbook\' />
         </form>
         `;
     };
     const createHTMLforWeights = () => {
-        $(".export-excel-weighted-option").remove();
-        if (grnState.workbook.sheetType !== "weighted") {
-            return `
-            <li class=\'export-excel-weighted-option\'>
-                <input type=\'radio\' checked=\"true\" name=\'network-weights\' value=\"unweighted\" id=\'exportExcelUnweightedRadio\' class=\'export-radio\' />
-                <label for=\'exportExcelUnweightedRadio\' id=\'exportExcelUnweighted\' class=\'export-radio-label\' >
-                    Unweighted
-                </label>
-            </li>`;
-        } else {
-            return `
-            <li class=\'export-excel-weighted-option\'>
-                <input type=\'radio\' checked=\"true\" name=\'network-weights\' value=\"weighted\" id=\'exportExcelWeightedRadio\' class=\'export-radio\' />
-                <label for=\'exportExcelWeightedRadio\' id=\'exportExcelWeighted\' class=\'export-radio-label\' >
-                    Weighted
-                </label>
-            </li>
-            <li class=\'export-excel-weighted-option\'>
-                <input type=\'radio\' name=\'network-weights\' value=\"unweighted\" id=\'exportExcelUnweightedRadio\' class=\'export-radio\' />
-                <label for=\'exportExcelUnweightedRadio\' id=\'exportExcelUnweighted\' class=\'export-radio-label\' >
-                    Unweighted
-                </label>
-            </li>
-            `;
-        }
+        // $(".export-excel-weighted-option").remove();
+        return `
+        <li class=\'export-excel-weighted-option\'>
+            <input type=\'radio\' ${grnState.workbook.sheetType === "weighted" ? "checked" : "disabled"}=\"true\" name=\'network-weights\' value=\"weighted\" id=\'exportExcelWeightedRadio\' class=\'export-radio\' />
+            <label for=\'exportExcelWeightedRadio\' id=\'exportExcelWeighted\' class=\'export-radio-label ${grnState.workbook.sheetType !== "weighted" && "disabled"}\' >
+                Weighted
+            </label>
+        </li>
+        <li class=\'export-excel-weighted-option\'>
+            <input type=\'radio\' ${grnState.workbook.sheetType !== "weighted" && "checked=\"true\""} name=\'network-weights\' value=\"unweighted\" id=\'exportExcelUnweightedRadio\' class=\'export-radio\' />
+            <label for=\'exportExcelUnweightedRadio\' id=\'exportExcelUnweighted\' class=\'export-radio-label\' >
+                Unweighted
+            </label>
+        </li>`;
     };
 
-    const createHTMLforExpressionSheets = (source) => {
-        $(".export-excel-expression-sheet-option").remove();
+    const createHTMLforSheets = (source) => {
+        $(".export-excel-workbook-sheet-option").remove();
         // check if user updated data is selected
         let result =  `
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' name=\'expressionSheets\' checked=\"true\" value=\"select all\" id=\'exportExcelExpression-All\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-All\' id=\'exportExcelExpression-All-label\' class=\'export-checkbox-label\' >
-                    All Expression Sheets
+            <li class=\'export-excel-workbook-sheet-option export-excel-workbook-sheet-option-subheader\'>
+                <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"select all\" id=\'exportExcelWorkbookSheet-All\' class=\'export-checkbox\' />
+                <label for=\'exportExcelWorkbookSheet-All\' id=\'exportExcelWorkbookSheet-All-label\' class=\'export-checkbox-label\' >
+                    Select All
+                </label>
+            </li>
+
+            <p class=\'export-excel-workbook-sheet-option-subheader\'> Network Sheets </p>
+            `;
+        const optionalAdditionalSheets = ["optimization_parameters", "production_rates", "degradation_rates", "threshold_b"];
+        let networks = [
+            (grnState.workbook.networkOptimizedWeights !== undefined && "network_optimized_weights"),
+            (grnState.workbook.network !== undefined && "network"),
+            (grnState.workbook.networkWeights !== undefined && "network_weights")];
+        networks = networks.filter(x => x !== false);
+        let additionalsheets = grnState.workbook.twoColumnSheets ? [
+            ...Object.keys(grnState.workbook.twoColumnSheets),
+            (grnState.workbook.meta2 !== undefined && "optimization_diagnostics")
+        ] : [
+            (grnState.workbook.meta2 !== undefined && "optimization_diagnostics")
+        ];
+        additionalsheets = additionalsheets.filter(x => (x !== false && -1 !== optionalAdditionalSheets.indexOf(x)));
+        additionalsheets = [...optionalAdditionalSheets, ...additionalsheets].sort();
+        additionalsheets = [...(new Set(additionalsheets))];
+        for (let network of networks) {
+            result = result + `
+            <li class=\'export-excel-workbook-sheet-option\'>
+                <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"${network}\" id=\'exportExcelWorkbookSheet-${network}\' class=\'export-checkbox\' />
+                <label for=\'exportExcelWorkbookSheet-${network}\' id=\'exportExcelWorkbookSheet-${network}-label\' class=\'export-checkbox-label\' >
+                    ${network}
                 </label>
             </li>
             `;
+        }
         if (source === "userInput") {
-            for (let expression in grnState.workbook.expression) {
+            result += grnState.workbook.expressionNames ? "<p class=\'export-excel-workbook-sheet-option-subheader\'> Expression Sheets </p>" : "";
+            if (grnState.workbook.expressionNames) {
+                for (let expression of grnState.workbook.expressionNames) {
+                    result += `
+                    <li class=\'export-excel-workbook-sheet-option\'>
+                        <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"${expression}\" id=\'exportExcelWorkbookSheet-${expression}\' class=\'export-checkbox\' />
+                        <label for=\'exportExcelWorkbookSheet-${expression}\' id=\'exportExcelWorkbookSheet-${expression}-label\' class=\'export-checkbox-label\' >
+                            ${expression}
+                        </label>
+                    </li>
+                    `;
+                }
+            }
+            result += "<p class=\'export-excel-workbook-sheet-option-subheader\'> Additional Sheets </p>";
+            for (let sheet of additionalsheets) {
                 result = result + `
-                <li class=\'export-excel-expression-sheet-option\'>
-                    <input type=\'checkbox\' name=\'expressionSheets\' checked=\"true\" value=\"${expression}\" id=\'exportExcelExpression-${expression}\' class=\'export-checkbox\' />
-                    <label for=\'exportExcelExpression-${expression}\' id=\'exportExcelExpression-${expression}-label\' class=\'export-checkbox-label\' >
-                        ${expression}
+                <li class=\'export-excel-workbook-sheet-option\'>
+                    <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"${sheet}\" id=\'exportExcelWorkbookSheet-${sheet}\' class=\'export-checkbox\' />
+                    <label for=\'exportExcelWorkbookSheet-${sheet}\' id=\'exportExcelWorkbookSheet-${sheet}-label\' class=\'export-checkbox-label\' >
+                        ${sheet}
                     </label>
                 </li>
                 `;
             }
-        } else if (source === "Dahlquist_2018") {
-            // if the source is from a database
-            result = result +  `
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' name=\'expressionSheets\' checked=\"true\" value=\"Dahlquist_2018_dcin5\" id=\'exportExcelExpression-Dahlquist_2018_dcin5\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Dahlquist_2018_dcin5\' id=\'exportExcelExpression-Dahlquist_2018_dcin5-label\' class=\'export-checkbox-label\' >
-                    Dahlquist_2018_dcin5
-                </label>
-            </li>
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' checked=\"true\" name=\'expressionSheets\' value=\"Dahlquist_2018_dgln3\" id=\'exportExcelExpression-Dahlquist_2018_dgln3\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Dahlquist_2018_dgln3\' id=\'exportExcelExpression-Dahlquist_2018_dgln3-label\' class=\'export-checkbox-label\' >
-                    Dahlquist_2018_dgln3
-                </label>
-            </li>
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' checked=\"true\" name=\'expressionSheets\' value=\"Dahlquist_2018_dhap4\" id=\'exportExcelExpression-Dahlquist_2018_dhap4\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Dahlquist_2018_dhap4\' id=\'exportExcelExpression-Dahlquist_2018_dhap4-label\' class=\'export-checkbox-label\' >
-                    Dahlquist_2018_dhap4
-                </label>
-            </li>
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' checked=\"true\" name=\'expressionSheets\' value=\"Dahlquist_2018_dzap1\" id=\'exportExcelExpression-Dahlquist_2018_dzap1\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Dahlquist_2018_dzap1\' id=\'exportExcelExpression-Dahlquist_2018_dzap1-label\' class=\'export-checkbox-label\' >
-                    Dahlquist_2018_dzap1
-                </label>
-            </li>
-            <div class=\'expression-db-loader\'></div>
-            <div class=\'expression-db-loader-text\'>Expression Database is Loading</div>
-            `;
-        } else if (source === "Kitagawa_2002") {
-            // if the source is from a database
-            result = result +  `
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' checked=\"true\" name=\'expressionSheets\' value=\"Kitagawa_2002_wt\" id=\'exportExcelExpression-Kitagawa_2002_wt\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Kitagawa_2002_wt\' id=\'exportExcelExpression-Kitagawa_2002_wt-label\' class=\'export-checkbox-label\' >
-                    Kitagawa_2002_wt
-                </label>
-            </li>
-            <div class=\'expression-db-loader\'></div>
-            <div class=\'expression-db-loader-text\'>Expression Database is Loading</div>
-            `;
-        } else if (source === "Thorsen_2007") {
-            // if the source is from a database
-            result = result +  `
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' checked=\"true\" name=\'expressionSheets\' value=\"Thorsen_2007_wt\" id=\'exportExcelExpression-Thorsen_2007_wt\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Thorsen_2007_wt\' id=\'exportExcelExpression-Thorsen_2007_wt-label\' class=\'export-checkbox-label\' >
-                    Thorsen_2007_wt
-                </label>
-            </li>
-            <div class=\'expression-db-loader\'></div>
-            <div class=\'expression-db-loader-text\'>Expression Database is Loading</div>
-            `;
-        } else if (source === "Barreto_2012") {
+        } else {
             // if the source is from a database
-            result = result + `
-            <li class=\'export-excel-expression-sheet-option\'>
-                <input type=\'checkbox\' checked=\"true\" name=\'expressionSheets\' value=\"Barreto_2012_wt\" id=\'exportExcelExpression-Barreto_2012_wt\' class=\'export-checkbox\' />
-                <label for=\'exportExcelExpression-Barreto_2012_wt\' id=\'exportExcelExpression-Barreto_2012_wt-label\' class=\'export-checkbox-label\' >
-                Barreto_2012_wt
-                </label>
-            </li>
+            result += "<p class=\'export-excel-workbook-sheet-option-subheader\'> Expression Sheets </p>";
+            const expressionSheets = grnState.database.expressionDatasets.filter(s => s.includes(source));
+            for (let sheet of expressionSheets) {
+                result += `
+                <li class=\'export-excel-workbook-sheet-option\'>
+                    <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"${sheet.slice(sheet.lastIndexOf("_") + 1) + "_log2_expression"}\" id=\'exportExcelWorkbookSheet-${sheet}\' class=\'export-checkbox\' />
+                    <label for=\'exportExcelWorkbookSheet-${sheet}\' id=\'exportExcelWorkbookSheet-${sheet}-label\' class=\'export-checkbox-label\' >
+                        ${sheet.slice(sheet.lastIndexOf("_") + 1) + "_log2_expression"}
+                    </label>
+                </li>`;
+            }
+
+            result += "<p class=\'export-excel-workbook-sheet-option-subheader\'> Additional Sheets </p>";
+            for (let sheet of additionalsheets) {
+                result += `
+                <li class=\'export-excel-workbook-sheet-option\'>
+                    <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"${sheet}\" id=\'exportExcelWorkbookSheet-${sheet}\' class=\'export-checkbox\' />
+                    <label for=\'exportExcelWorkbookSheet-${sheet}\' id=\'exportExcelWorkbookSheet-${sheet}-label\' class=\'export-checkbox-label\' >
+                        ${sheet}
+                    </label>
+                </li>
+                `;
+            }
+            result += `
             <div class=\'expression-db-loader\'></div>
             <div class=\'expression-db-loader-text\'>Expression Database is Loading</div>
             `;
@@ -382,33 +504,90 @@ export const upload = function () {
         return result;
     };
 
-    const handleExportExcelButtonContinue = () => {
-        const weight = $("input[name=network-weights]:checked")[0].value;
-        const source = $("input[name=expressionSource]:checked")[0].value;
-        $("#exportExcelForm1").remove();
-        // $("#exportExcelForm1")[0].style = "display:none;";
-        $("#exportExcelQuestions-containter").append(createHTMLforForm2);
-        $("#exportExcelExpressionSheets").html("Select Expression Sheets:");
-        $("#export-excel-expression-sheet-list").append(createHTMLforExpressionSheets(source));
-        $("#exportExcelButton").on("click", performExport("export-to-excel", "xlsx", weight, source));
+    const createHTMLforModalButtons = (isInitialModal) => {
+        return `
+            <div id=\'exportExcelFooter\' class=\'modal-footer-div\'>
+                ${ !isInitialModal ?
+                    `<div>
+                        <input type=\'button\' class=\'btn btn-default\' id=\'Export-Excel-Button-Back\' value=\'Back\'  />
+                    </div>` : ""
+                }
+                <div>
+                    <input type=\'button\' class=\'btn btn-default\' id=\'Export-Excel-Button${isInitialModal ? "-Continue" : ""}\' />
+                    <input type=\'button\' class=\'btn btn-default\' data-dismiss=\'modal\' value=\'Cancel\'  />
+                <div>
+            </div>
+        `;
     };
 
-    var displayExportExcelModal = function () {
+    var handleExportExcelModal = function () {
+        $("#exportExcelForm1").remove();
         $("#exportExcelForm2").remove();
+        $("#exportExcelFooter").remove();
         $("#exportExcelQuestions-containter").append(createHTMLforForm1);
-        $("#exportExcelNetwork").html("Select the workbooks export type:");
-        $("#export-excel-weights-list").append(createHTMLforWeights());
+        $("#exportExcelFooter-container").append(createHTMLforModalButtons(true));
 
+        $("#exportExcelNetwork").html("Select the edge type:");
+        $("#export-excel-weights-list").append(createHTMLforWeights());
+        $("#Export-Excel-Button-Continue").prop("value", "Continue");
         $("#exportExcelExpressionSources").html("Select the Expression Data Source:");
         $("#exportExcelExpressionSource-userInput").html(grnState.name);
-        $("#exportExcelExpressionSource-Dahlquist").html("Dahlquist_2018");
-        $("#exportExcelExpressionSource-Kitagawa").html("Kitagawa_2002");
-        $("#exportExcelExpressionSource-Thorsen").html("Thorsen_2007");
-        $("#exportExcelExpressionSource-Barreto").html("Barreto_2012");
-        $("#exportExcelContinueButton").on("click", () => handleExportExcelButtonContinue());
+    };
+
+    var handleWorkbookSheetCheckboxBehaviour = () => {
+        $("input[name=workbookSheets]").not($("#exportExcelWorkbookSheet-All")).on("click", ()=>{
+            const selectAll = $("#exportExcelWorkbookSheet-All");
+            const allSheets = $("input[name=workbookSheets]");
+            if (selectAll[0].checked) {
+                for (let i in allSheets) {
+                    if (typeof allSheets[i] === "object") {
+                        if (allSheets[i].checked !==  selectAll[0].checked) {
+                            selectAll[0].checked = false;
+                        }
+                    }
+                }
+            }
+        });
+        $("#exportExcelWorkbookSheet-All").on("click", ()=>{
+            const allSheets = $("input[name=workbookSheets]");
+            const selectAll = $("#exportExcelWorkbookSheet-All");
+            for (let i in allSheets) {
+                if (typeof allSheets[i] === "object") {
+                    allSheets[i].checked = selectAll[0].checked;
+                }
+            }
+        });
+    };
+
+    var handleExportExcelButtonContinue = () => {
+        const weight = $("input[name=network-weights]:checked")[0].value;
+        const source = $("input[name=expressionSource]:checked")[0].value;
+        $("#exportExcelForm1").remove();
+        $("#exportExcelFooter").remove();
+        $("#exportExcelFooter-container").append(createHTMLforModalButtons(false));
+        $("#Export-Excel-Button").prop("value", "Export Workbook");
+        $("#exportExcelQuestions-containter").append(createHTMLforForm2);
+        $("#exportExcelWorkbookSheets").html("Select Workbook Sheets to Export:");
+        $("#export-excel-workbook-sheet-list").append(createHTMLforSheets(source));
+        handleWorkbookSheetCheckboxBehaviour();
+        $("#Export-Excel-Button-Back").on("click", () => {
+            handleExportExcelModal();
+            $("input[name=network-weights]").removeAttr("checked");
+            $("input[name=network-weights][value=" + weight + "]").prop("checked", true);
+            $("input[name=expressionSource]").removeAttr("checked");
+            $("input[name=expressionSource][value=" + source + "]").prop("checked", true);
+            $("#Export-Excel-Button-Continue").on("click", () => handleExportExcelButtonContinue());
+        });
+        $("#Export-Excel-Button").on("click", performExport("export-to-excel", "xlsx", weight, source));
+    };
+
+    var displayExportExcelModal = function () {
+        handleExportExcelModal();
+        $("#Export-Excel-Button-Continue").on("click", () => handleExportExcelButtonContinue());
         $("#exportExcelModal").modal("show");
     };
 
+
     var performExcelExport = function () {
         return function () {
             if (!$(this).parent().hasClass("disabled")) {
@@ -417,13 +596,10 @@ export const upload = function () {
         };
     };
 
-    // $("#exportAsExcelWkbk").click(performExport("export-to-excel", "xlsx", "unweighted"));
     $("#exportAsUnweightedSif").on("click", performExport("export-to-sif", "sif", "unweighted"));
     $("#exportAsWeightedSif").on("click", performExport("export-to-sif", "sif", "weighted"));
     $("#exportAsUnweightedGraphMl").on("click", performExport("export-to-graphml", "graphml", "unweighted"));
     $("#exportAsWeightedGraphMl").on("click", performExport("export-to-graphml", "graphml", "weighted"));
-    // $("#exportAsUnweightedExcel").on("click", performExport("export-to-excel", "xlsx", "unweighted"));
-    // $("#exportAsWeightedExcel").on("click", performExport("export-to-excel", "xlsx", "weighted"));
     $("#exportAsExcel").on("click", performExcelExport());
 
 };