grnsight 6.0.0 → 6.0.4

package/test/test.js

@@ -526,8 +526,8 @@ var twoColumnIdError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var twoColumnIdErrorCount = 0;
-    for (let page in workbook.test) {
-        twoColumnIdErrorCount += workbook.test[page].errors.filter(function (x) {
+    for (let page in workbook.twoColumnSheets) {
+        twoColumnIdErrorCount += workbook.twoColumnSheets[page].errors.filter(function (x) {
             return x.errorCode === "MISLABELED_ID_CELL";
         }).length;
     }
@@ -538,8 +538,8 @@ var additionalSheetIncorrectColumnHeaderError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var additionalSheetIncorrectColumnHeaderErrorCount = 0;
-    for (let page in workbook.test) {
-        additionalSheetIncorrectColumnHeaderErrorCount  += workbook.test[page].errors.filter(
+    for (let page in workbook.twoColumnSheets) {
+        additionalSheetIncorrectColumnHeaderErrorCount  += workbook.twoColumnSheets[page].errors.filter(
             (x) => x.errorCode === "INCORRECT_COLUMN_HEADER").length;
     }
     additionalSheetIncorrectColumnHeaderErrorCount += workbook.meta.errors.filter(
@@ -555,8 +555,8 @@ var additionalSheetMissingColumnHeaderError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var additionalSheetMissingColumnHeaderErrorCount = 0;
-    for (let page in workbook.test) {
-        additionalSheetMissingColumnHeaderErrorCount += workbook.test[page].errors.filter(
+    for (let page in workbook.twoColumnSheets) {
+        additionalSheetMissingColumnHeaderErrorCount += workbook.twoColumnSheets[page].errors.filter(
             (x) => x.errorCode === "MISSING_COLUMN_HEADER").length;
     }
     additionalSheetMissingColumnHeaderErrorCount += workbook.meta.errors.filter(
@@ -572,8 +572,8 @@ var twoColumnInvalidGeneTypeError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var twoColumnInvalidGeneTypeErrorCount = 0;
-    for (let page in workbook.test) {
-        twoColumnInvalidGeneTypeErrorCount += workbook.test[page].errors.filter(function (x) {
+    for (let page in workbook.twoColumnSheets) {
+        twoColumnInvalidGeneTypeErrorCount += workbook.twoColumnSheets[page].errors.filter(function (x) {
             return x.errorCode === "INVALID_GENE_TYPE";
         }).length;
     }
@@ -584,8 +584,8 @@ var twoColumnInvalidValueError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var twoColumnInvalidValueErrorCount = 0;
-    for (let page in workbook.test) {
-        twoColumnInvalidValueErrorCount  += workbook.test[page].errors.filter(function (x) {
+    for (let page in workbook.twoColumnSheets) {
+        twoColumnInvalidValueErrorCount  += workbook.twoColumnSheets[page].errors.filter(function (x) {
             return x.errorCode === "INVALID_VALUE";
         }).length;
     }
@@ -596,8 +596,8 @@ var twoColumnInvalidGeneLengthError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var twoColumnInvalidGeneLengthErrorCount = 0;
-    for (let page in workbook.test) {
-        twoColumnInvalidGeneLengthErrorCount  += workbook.test[page].errors.filter(function (x) {
+    for (let page in workbook.twoColumnSheets) {
+        twoColumnInvalidGeneLengthErrorCount  += workbook.twoColumnSheets[page].errors.filter(function (x) {
             return x.errorCode === "INVALID_GENE_LENGTH";
         }).length;
     }
@@ -608,8 +608,8 @@ var twoColumnSpecialCharacterError = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var twoColumnSpecialCharacterErrorCount = 0;
-    for (let page in workbook.test) {
-        twoColumnSpecialCharacterErrorCount += workbook.test[page].errors.filter(function (x) {
+    for (let page in workbook.twoColumnSheets) {
+        twoColumnSpecialCharacterErrorCount += workbook.twoColumnSheets[page].errors.filter(function (x) {
             return x.errorCode === "INVALID_CHARACTER";
         }).length;
     }
@@ -622,8 +622,8 @@ var additionalSheetExtraneousDataWarning = function (input, frequency) {
     var sheet = xlsx.parse(input);
     var workbook = parseAdditionalSheet(sheet);
     var additionalSheetExtraneousDataWarningCount = 0;
-    for (let page in workbook.test) {
-        additionalSheetExtraneousDataWarningCount  += workbook.test[page].warnings.filter(function (x) {
+    for (let page in workbook.twoColumnSheets) {
+        additionalSheetExtraneousDataWarningCount  += workbook.twoColumnSheets[page].warnings.filter(function (x) {
             return x.warningCode === "EXTRANEOUS_DATA";
         }).length;
     }
@@ -716,7 +716,26 @@ var invalidMSEDataWarning = function (input, frequency) {
 var importExportReImportNoErrorsOrWarnings = function (input) {
     var sheet = xlsx.parse(input);
     var inputWorkbook = spreadsheetController.crossSheetInteractions(sheet);
-    inputWorkbook["exportExpression"] = inputWorkbook.expression;
+    inputWorkbook.exportSheets = {
+        "optimization_parameters": inputWorkbook.meta,
+        expression: inputWorkbook.expression,
+        networks: {}
+    };
+    if (inputWorkbook.network) {
+        inputWorkbook.exportSheets.networks["network"] = inputWorkbook.network;
+    }
+    if (inputWorkbook.networkOptimizedWeights) {
+        inputWorkbook.exportSheets.networks["network_optimized_weights"] = inputWorkbook.networkOptimizedWeights;
+    }
+    if (inputWorkbook.networkWeights) {
+        inputWorkbook.exportSheets.networks["network_weights"] = inputWorkbook.networkWeights;
+    }
+    if (inputWorkbook.twoColumnSheets) {
+        inputWorkbook.exportSheets["two_column_sheets"] = inputWorkbook.twoColumnSheets;
+    }
+    if (inputWorkbook.meta2) {
+        inputWorkbook.exportSheets["optimization_diagnostics"] = inputWorkbook.meta2;
+    }
     var exportedWorkbook = exportController.grnsightToXlsx(inputWorkbook);
     var sheet2 = xlsx.parse(exportedWorkbook);
     var reImportedWorkbook = spreadsheetController.crossSheetInteractions(sheet2);
@@ -726,8 +745,26 @@ var importExportReImportNoErrorsOrWarnings = function (input) {
 var importFileSameAsExportFile = function (input) {
     var sheet = xlsx.parse(input);
     var inputWorkbook = spreadsheetController.crossSheetInteractions(sheet);
-    inputWorkbook["exportExpression"] = inputWorkbook.expression;
-    inputWorkbook["exportNetworkType"] = inputWorkbook.sheetType;
+    inputWorkbook.exportSheets = {
+        "optimization_parameters": inputWorkbook.meta,
+        expression: inputWorkbook.expression,
+        networks: {}
+    };
+    if (inputWorkbook.network) {
+        inputWorkbook.exportSheets.networks["network"] = inputWorkbook.network;
+    }
+    if (inputWorkbook.networkOptimizedWeights) {
+        inputWorkbook.exportSheets.networks["network_optimized_weights"] = inputWorkbook.networkOptimizedWeights;
+    }
+    if (inputWorkbook.networkWeights) {
+        inputWorkbook.exportSheets.networks["network_weights"] = inputWorkbook.networkWeights;
+    }
+    if (inputWorkbook.twoColumnSheets) {
+        inputWorkbook.exportSheets["two_column_sheets"] = inputWorkbook.twoColumnSheets;
+    }
+    if (inputWorkbook.meta2) {
+        inputWorkbook.exportSheets["optimization_diagnostics"] = inputWorkbook.meta2;
+    }
     var exportedWorkbook = exportController.grnsightToXlsx(inputWorkbook);
     var sheet2 = xlsx.parse(exportedWorkbook);
     sheet.sort((a, b) => (a.name > b.name) ? 1 : -1);

package/web-client/public/js/api/grnsight-api.js

@@ -1,124 +1,88 @@
-import {responseCustomWorkbookData} from "../setup-load-and-import-handlers";
-
-// Expression DB Access Functions
-const buildExpressionTimepointsString = function (selection) {
-    let timepoints = "";
-    selection.timepoints.forEach(x => timepoints += (x + ","));
-    return timepoints.substring(0, timepoints.length - 1);
-};
-const buildExpressionGeneQuery = function (workbookGenes) {
-    let genes = "";
-    workbookGenes.forEach(x => genes += (x.name + ","));
-    return genes.substring(0, genes.length - 1);
+import { responseCustomWorkbookData } from "../setup-load-and-import-handlers";
+// General DB Access Functions
+const buildQueryURL = function(path, parameters) {
+  const searchParams = new URLSearchParams("");
+  for (let p in parameters) {
+    searchParams.append(p, parameters[p]);
+  }
+  return `${path}?${searchParams.toString()}`;
 };
 
-const buildExpressionURL = function (selection, genes) {
-    const baseQuery = `expressiondb?dataset=${selection.dataset}&genes=${buildExpressionGeneQuery(genes)}`;
-    return selection.timepoints ?
-    `${baseQuery}&timepoints=${buildExpressionTimepointsString(selection)}` :
-    baseQuery;
+const responseData = (database, formData, queryURL) => {
+  return new Promise(function(resolve) {
+    const uploadRoute = queryURL;
+    const fullUrl = [$(".service-root").val(), uploadRoute].join("/");
+    (formData
+      ? $.ajax({
+          url: fullUrl,
+          data: formData,
+          processData: false,
+          contentType: false,
+          type: "GET",
+          crossDomain: true,
+        })
+      : $.getJSON(fullUrl)
+    )
+      .done((data) => {
+        resolve(data);
+      })
+      .error(function() {
+        console.log(
+          `Error in accessing ${database} database. Result may just be loading.`
+        );
+      });
+  });
 };
 
-const responseExpressionData = (formData, queryURL) => {
-    return new Promise(function (resolve) {
-        const uploadRoute = queryURL;
-        const fullUrl = [ $(".service-root").val(), uploadRoute ].join("/");
-        (formData ?
-            $.ajax({
-                url: fullUrl,
-                data: formData,
-                processData: false,
-                contentType: false,
-                type: "GET",
-                crossDomain: true
-            }) :
-            $.getJSON(fullUrl)
-            ).done((expressionData) => {
-                resolve(expressionData);
-            }).error(console.log("Error in accessing expression database. Result may just be loading."));
-    });
-};
+// Expression DB Access Functions
 
 const queryExpressionDatabase = (query) => {
-    let queryURL = buildExpressionURL({dataset: query.dataset}, query.genes);
-    return responseExpressionData("", queryURL);
+  const queryURL = buildQueryURL("expressiondb", query);
+  return responseData("expression", "", queryURL);
 };
 
 // Network DB Access Functions
 
-const buildNetworkGenesQuery = (genes) => {
-    let result = "";
-    for (let gene in genes) {
-        result += `${gene},`;
-    }
-    return result.substring(0, result.length - 1);
+const queryNetworkDatabase = (query) => {
+  const queryURL = buildQueryURL("networkdb", query);
+  return responseData("network", "", queryURL);
 };
 
-const buildNetworkURL = function (queryType, queryInfo) {
-    let baseQuery = `networkdb?type=${queryType}`;
-    if (queryInfo !== null) {
-        for (let header in queryInfo) {
-            if (header === "genes") {
-                baseQuery += `&${header}=${buildNetworkGenesQuery(queryInfo[header])}`;
-            } else {
-                baseQuery += `&${header}=${queryInfo[header]}`;
-            }
-        }
-    }
-    return baseQuery;
-};
+// Upload Custom Workbook Functions
 
-const responseNetworkData = (formData, queryURL) => {
-    return new Promise(function (resolve) {
-        const uploadRoute = queryURL;
-        const fullUrl = [ $(".service-root").val(), uploadRoute ].join("/");
-        (formData ?
-            $.ajax({
-                url: fullUrl,
-                data: formData,
-                processData: false,
-                contentType: false,
-                type: "GET",
-                crossDomain: true
-            }) :
-            $.getJSON(fullUrl)
-            ).done((networkData) => {
-                resolve(networkData);
-            }).error(console.log("Error in accessing network database. Result may just be loading."));
-    });
+const uploadCustomWorkbook = (workbook, grnState) => {
+  const queryURL = buildQueryURL("upload-custom-workbook", workbook);
+  return responseCustomWorkbookData(grnState, queryURL, workbook.name);
 };
 
-const queryNetworkDatabase = (query) => {
-    let queryURL = buildNetworkURL(query.type, query.info);
-    return responseNetworkData("", queryURL);
-};
+const constructFullUrl = (queryURL) =>
+  [$(".service-root").val(), queryURL].join("/");
 
-// Upload Custom Workbook Functions
-const buildCustomWorkbookURL = (name, genes, links) => {
-    let baseQuery = `upload-custom-workbook?name=${name}`;
-    let genesString = "";
-    let linksString = "";
-    let genesByIndex = {};
-    let i = 0;
-    for (let gene in genes) {
-        genesString += `${genes[gene]},`;
-        genesByIndex[gene] = i;
-        i++;
-    }
-    for (let regulator in links) {
-        for (let target of links[regulator]) {
-            linksString += `${genesByIndex[regulator]}->${genesByIndex[target]},`;
-        }
-    }
-    baseQuery += `&genes=${genesString.substring(0, genesString.length - 1)}`;
-    baseQuery += `&links=${linksString.substring(0, linksString.length - 1)}`;
-    return baseQuery;
-};
+const getWorkbookFromForm = (formData, queryURL) => {
+  const fullUrl = constructFullUrl(queryURL);
 
-const uploadCustomWorkbook = (workbook, grnState) => {
-    let queryURL = buildCustomWorkbookURL(workbook.name, workbook.genes, workbook.links);
-    return responseCustomWorkbookData(grnState, queryURL, workbook.name);
+  // The presence of formData is taken to indicate a POST.
+  return formData
+    ? $.ajax({
+        url: fullUrl,
+        data: formData,
+        processData: false,
+        contentType: false,
+        type: "POST",
+        crossDomain: true,
+      })
+    : $.getJSON(fullUrl);
 };
 
+const getWorkbookFromUrl = (queryURL) => {
+  const fullUrl = constructFullUrl(queryURL);
+  return $.getJSON(fullUrl);
+};
 
-export {queryExpressionDatabase, queryNetworkDatabase, uploadCustomWorkbook};
+export {
+  queryExpressionDatabase,
+  queryNetworkDatabase,
+  uploadCustomWorkbook,
+  getWorkbookFromForm,
+  getWorkbookFromUrl,
+};

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

@@ -6,7 +6,7 @@ export const GREY_EDGES_DASHED_MENU = "#grey-edges-dashed-menu";
 export const GREY_EDGES_DASHED_SIDEBAR = "#dashedGrayLineButton";
 
 export const CREATE_NETWORK_CLASS = ".create-network";
-export const CREATE_NETWORK_MODAL = "#createNetworkModal";
+export const CREATE_NETWORK_MODAL = "#generateNetworkModal";
 
 export const UNWEIGHTED_DEMO_ID   = ".unweighted";
 export const UNWEIGHTED_DEMO_PATH = "demo/unweighted";

package/web-client/public/js/{createNetwork.js → generateNetwork.js}

@@ -1,15 +1,24 @@
+/* eslint-disable max-len */
 import {CREATE_NETWORK_CLASS, CREATE_NETWORK_MODAL} from "./constants";
 import { queryNetworkDatabase, uploadCustomWorkbook } from "./api/grnsight-api";
 import { grnState } from "./grnstate";
 
-export const createNetwork = function () {
+export const generateNetwork = function () {
+    const GENE_EXCEPTIONS = {
+        "DUR1,2" : "DUR12",
+        "IMP2'" : "IMP21",
+        "ARG5,6" : "ARG56",
+        "ADE5,7" : "ADE57",
+        "MF(ALPHA)1" : "YPL187W",
+        "MF(ALPHA)2" : "YGL089C"
+    };
     const createHTMLforForm = (sources) => {
         let result =  `
-            <div id=\'createNetworkFormContainer\' '>
-                <h2 id=\'createNetwork\'>Create Network</h2>
-        <div class=\'form-group\'>
-            <label for=\'network-source\' id=\'network-source-label\'>Network Source</label>
-            <select class=\'network-dropdown btn btn-default\' id=\'network-source\'>
+            <div id=\'generateNetworkFormContainer\' '>
+                <h2 id=\'generateNetwork\'>Generate Network</h2>
+                <div class=\'form-group\'>
+                    <label for=\'network-source\' id=\'network-source-label\'>Network Source</label>
+                    <select class=\'network-dropdown btn btn-default\' id=\'network-source\'>
             `;
         if (sources.length !== 1) {
             result += "<option value=\'none\' selected=\'true\' disabled>Select Network Source</option>";
@@ -24,10 +33,10 @@ export const createNetwork = function () {
             `;
         }
         result += `</select>
-                   <p>Warning: changing network source will remove all current genes in network</p>
+                   <p>Warning: changing network source will clear the list of genes below.</p>
                 </div>
         <div class=\'form-group\' id=\'getNetworkGenesForm\'>
-            <form id=\'getNetworkGenesForm\'>
+            <form id=\'getNetworkGenesForm\' class=\'NetworkGenesForm\' >
                 <label for=\'network-search-bar\' id=\'network-source-label\'>Select genes</label>
                 <input type=\'text\' id=\'network-search-bar\' name=\'network-search-bar\'></input>
                 <button id=\'enter-search\' type=\'submit\' class=\'search-button btn btn-default\'>
@@ -37,10 +46,7 @@ export const createNetwork = function () {
         </div>
         <div id=\'selected-genes-container\'>
             <div id=\'selected-genes\'>
-                <p>Added genes go here! Click on a gene to remove it</p>
-            </div>
-        </div>
-        <button id=\'submit-network\' class=\'btn btn-default\'>Create Network</input>
+                <p>Added genes go here! Click on a gene to remove it.</p>
             </div>
         `;
         return result;
@@ -78,28 +84,38 @@ export const createNetwork = function () {
         }
     };
 
+    const validGene = function (gene) {
+        if (/^[A-Z0-9_-]{1,12}$/.test(gene)) {
+            return gene;
+        }
+        if (Object.keys(GENE_EXCEPTIONS).includes(gene)) {
+            return GENE_EXCEPTIONS[gene];
+        }
+        return "";
+    };
     const addGene = function () {
-        let gene = `${$("#network-search-bar").val()}`.toUpperCase();
+        const searchGene = `${$("#network-search-bar").val()}`.toUpperCase();
         $("#network-search-bar").val("");
-        if (!(/^[A-Z0-9_-]{1,12}$/.test(gene))) {
-            alert(`Gene: ${gene} is not to GRNsight specifications. Genes must be 12 characters or less,
+        const gene = validGene(searchGene);
+        if (gene === "") {
+            alert(`Gene: ${searchGene} is not to GRNsight specifications. Genes must be 12 characters or less,
 containing "-", "_", and alpha-numeric characters only`);
         } else {
             let source = grnState.customWorkbook.source;
             let headers = {
                 type:"NetworkGeneFromSource",
-                info: {
-                    gene: gene,
-                    source:grnState.customWorkbook.sources[source].source,
-                    timestamp:grnState.customWorkbook.sources[source].timestamp.substring(0, 19).replace("T", " ")
-                }
+                gene: gene,
+                source:grnState.customWorkbook.sources[source].source,
+                timestamp:grnState.customWorkbook.sources[source].timestamp
             };
             queryNetworkDatabase(headers).then(function (response) {
                 if (response.geneId !== null && response.displayGeneId !== null) {
                     grnState.customWorkbook.genes[response.geneId] = response.displayGeneId;
                     displayCurrentGenes();
                 } else {
-                    alert(`Gene: ${gene} was not found in this database. Please check for any typos and try again.`);
+                    alert(
+                        `Gene: ${searchGene} was not found in this database. Please check for any typos and try again.`
+                    );
                 }
             }).catch(function (error) {
                 console.log(error.stack);
@@ -110,17 +126,31 @@ containing "-", "_", and alpha-numeric characters only`);
         }
     };
 
-    const displayCreateNetworkModal = function () {
-        $("#createNetworkFormContainer").remove();
+    const createHTMLforModalButtons = () => {
+        return `
+            <div id=\'generateNetworkFooter\' class=\'modal-footer-div\'>
+                <div>
+                    <input type=\'button\' class=\'btn btn-default\' id=\'submit-network\' value=\'Generate Network\'/>
+                    <input type=\'button\' class=\'btn btn-default\' data-dismiss=\'modal\' value=\'Cancel\'  />
+                </div>
+            </div>
+        `;
+    };
+
+    const displayGenerateNetworkModal = function () {
+        $("#generateNetworkFormContainer").remove();
+        $("#generateNetworkFooter").remove();
+        $("#generateNetworkFooter-container").append(createHTMLforModalButtons());
         grnState.customWorkbook = {
             genes : {},
-            source : null
+            source : null,
+            sources : null
         };
     // get sources from database
-        queryNetworkDatabase({type:"NetworkSource", info:null}).then(function (response) {
-            $("#createNetworkQuestions-container").append(createHTMLforForm(Object.keys(response.sources)));
+        queryNetworkDatabase({type:"NetworkSource"}).then(function (response) {
+            $("#generateNetworkQuestions-container").append(createHTMLforForm(Object.keys(response.sources)));
             grnState.customWorkbook.sources = response.sources;
-            grnState.customWorkbook.source = Object.keys(response.sources).length === 1 ?
+            grnState.customWorkbook.source = Object.keys(response.sources).length >= 1 ?
                 Object.keys(response.sources)[0] : null;
         }).catch(function (error) {
             console.log(error.stack);
@@ -133,7 +163,7 @@ containing "-", "_", and alpha-numeric characters only`);
     $("body").on("click", CREATE_NETWORK_CLASS, function (event) {
         event.preventDefault();
         event.stopPropagation();
-        displayCreateNetworkModal();
+        displayGenerateNetworkModal();
     });
 
     $("body").on("change", "#network-source", function (event) {
@@ -150,28 +180,25 @@ containing "-", "_", and alpha-numeric characters only`);
             alert(`GRNsight is only capable of handling 75 genes at most. Your proposed network contains
  ${genesAmount} genes. Please remove some genes from your proposed network.`);
         } else {
-
-            let source = grnState.customWorkbook.source;
-            let headers = {
-                type:"CreateNetwork",
-                info: {
-                    genes: grnState.customWorkbook.genes,
-                    source:grnState.customWorkbook.sources[source].source,
-                    timestamp:grnState.customWorkbook.sources[source].timestamp.substring(0, 19).replace("T", " ")
-                }
+            const genes = Object.keys(grnState.customWorkbook.genes).map(g => grnState.customWorkbook.genes[g]);
+            const source = grnState.customWorkbook.source;
+            const headers = {
+                type:"GenerateNetwork",
+                genes: genes.join(","),
+                source:grnState.customWorkbook.sources[source].source,
+                timestamp:grnState.customWorkbook.sources[source].timestamp
             };
             queryNetworkDatabase(headers).then(function (response) {
                 grnState.customWorkbook.links = response.links;
-                let genes = grnState.customWorkbook.genes;
-                let links = grnState.customWorkbook.links;
-                let genesAmount = Object.keys(genes).length;
-                let edgesAmount = Object.keys(links).length;
+                const links = Object.entries(grnState.customWorkbook.links);
+                const genesAmount = genes.length;
+                const edgesAmount = links.flatMap( (entry) => entry[1].map((target) => [entry[0], target])).length;
                 if (edgesAmount > 100) {
                     alert(`GRNsight is only capable of handling 100 edges at most. Your proposed network contains
  ${edgesAmount} regulatory connections. Please remove some genes from your proposed network.`);
                 } else {
-                    let name = `Custom Workbook: UnweightedGRN(${genesAmount} genes, ${edgesAmount} edges)`;
-                    let workbook = {name, genes, links};
+                    const name = `Custom Workbook: UnweightedGRN(${genesAmount} genes, ${edgesAmount} edges)`;
+                    const workbook = {name, genes, links : links.map( l => `${l[0]}->${l[1]}`).join(",")};
                     uploadCustomWorkbook(workbook, grnState);
                     $(CREATE_NETWORK_MODAL).modal("hide");
                 }

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

@@ -1,6 +1,6 @@
 import { displayStatistics } from "./graph-statistics"; // eslint-disable-line no-unused-vars
 import { upload } from "./upload";
-import { createNetwork } from "./createNetwork";
+import { generateNetwork } from "./generateNetwork";
 
 import { grnState } from "./grnstate";
 import { updateApp } from "./update-app";
@@ -10,4 +10,4 @@ setupHandlers(grnState);
 updateApp(grnState);
 
 upload();
-createNetwork();
+generateNetwork();