grnsight 7.1.1 → 7.2.0

package/.github/workflows/node.js.yml

@@ -0,0 +1,35 @@
+# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
+
+name: Node.js CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x, 22.x]
+
+    steps:
+    - uses: actions/checkout@v4
+    # install system dependencies needed by the 'canvas' package
+    - name: Install dependencies for canvas
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcairo2-dev libpango1.0-dev libjpeg62 libgif-dev librsvg2-dev
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: 'npm'
+        
+    - run: npm ci
+    - run: npm run lint 
+    - run: npm run build --if-present
+    - run: npm test
+
+    

package/README.md

@@ -1,7 +1,7 @@
 GRNsight
 ========
 [![DOI](https://zenodo.org/badge/16195791.svg)](https://zenodo.org/badge/latestdoi/16195791)
-[![Build Status](https://app.travis-ci.com/dondi/GRNsight.svg?branch=master)](https://app.travis-ci.com/dondi/GRNsight)
+[![Node.js CI](https://github.com/dondi/GRNsight/actions/workflows/node.js.yml/badge.svg)](https://github.com/dondi/GRNsight/actions/workflows/node.js.yml)
 [![Coverage Status](https://coveralls.io/repos/github/dondi/GRNsight/badge.svg?branch=master)](https://coveralls.io/github/dondi/GRNsight?branch=master)
 
 http://dondi.github.io/GRNsight/

package/database/network-database/schema.sql

@@ -20,6 +20,6 @@ CREATE TABLE gene_regulatory_network.network (
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
   FOREIGN KEY (regulator_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
-  FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network_testing.gene(gene_id, taxon_id),
-  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network_testing.source(time_stamp, source)
+  FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
+  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source)
 ); 

package/database/protein-protein-database/schema.sql

@@ -20,7 +20,7 @@ CREATE TABLE protein_protein_interactions.protein (
   molecular_weight FLOAT,
   PI FLOAT,
   taxon_id VARCHAR,
-  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions_testing.gene(gene_id, taxon_id)
+  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions.gene(gene_id, taxon_id)
 );
 
 CREATE TABLE protein_protein_interactions.physical_interactions (
@@ -30,8 +30,8 @@ CREATE TABLE protein_protein_interactions.physical_interactions (
   experiment_name VARCHAR,
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
-  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions_testing.protein(standard_name),
-  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions_testing.protein(standard_name),
-  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions_testing.source(time_stamp, source),
+  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions.protein(standard_name),
+  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions.protein(standard_name),
+  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source),
   CONSTRAINT unique_physical_interaction UNIQUE (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source)
 );

package/package.json

@@ -1,13 +1,14 @@
 {
   "name": "grnsight",
-  "version": "7.1.1",
+  "version": "7.2.0",
   "description": "Web app and service for visualizing models of gene regulatory networks",
   "directories": {
     "test": "test"
   },
   "dependencies": {
     "body-parser": "1.18.2",
-    "canvg": "2.0.0",
+    "canvas": "^2.11.2",
+    "canvg": "3.0.10",
     "cors": "2.8.1",
     "cytoscape": "2.7.14",
     "d3-v4-grid": "2.0.1",

package/server/controllers/demo-workbooks.js

@@ -515,7 +515,7 @@ var demoWorkbook1 = function (path, res, app) {
         },
         meta: {
             data: {
-                alpha: 0.002,
+                alpha: 0.02,
                 kk_max: 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
@@ -2679,7 +2679,7 @@ var demoWorkbook2 = function (path, res, app) {
         },
         meta: {
             data: {
-                alpha: 0.002,
+                alpha: 0.02,
                 kk_max: 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,

package/server/controllers/importers/sif.js

@@ -61,14 +61,15 @@ module.exports = function (sif) {
         if (allNumbers) {
             workbookType = constants.NETWORK_GRN_MODE;
         } else {
-            for (const relationship of relationships) {
-                if (relationship === "pp") {
-                    workbookType = constants.NETWORK_PPI_MODE;
-                    break;
-                } else if (relationship === "pd") {
-                    workbookType = constants.NETWORK_GRN_MODE;
-                    break;
-                }
+            let stringRelationships = relationships.filter(function (relationship) {
+                return !isNumber(relationship);
+            });
+            if (stringRelationships.every(rel => rel === "pp")) {
+                workbookType = constants.NETWORK_PPI_MODE;
+            } else if (stringRelationships.every(rel => rel === "pd")) {
+                workbookType = constants.NETWORK_GRN_MODE;
+            } else if (stringRelationships.every(rel => rel === "pp" || rel === "pd")) {
+                errors.push(sifConstants.errors.SIF_MIXED_RELATIONSHIP_TYPE_ERROR);
             }
         }
 

package/server/controllers/sif-constants.js

@@ -32,5 +32,12 @@ module.exports = {
             possibleCause: "GRNsight has detected stray data and/or extraneous blank rows in your SIF file. ",
             suggestedFix: "Please review the data and delete extraneous data from the file."
         },
+
+        SIF_MIXED_RELATIONSHIP_TYPE_ERROR: {
+            errorCode: "SIF_MIXED_RELATIONSHIP_TYPE_ERROR",
+            possibleCause: "The SIF importer detects a SIF file with mixed relationship types.",
+            suggestedFix: ["GRNsight only supports networks with a single relationship type.",
+                "Please review the relationships for consistency."].join(" ")
+        },
     },
 };

package/server/dals/expression-dal.js

@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
@@ -20,7 +20,7 @@ var sequelize = new Sequelize(
 const buildExpressionGenesQuery = function (geneString) {
     let genes = "";
     let geneList = geneString.split(",");
-    geneList.forEach(x => genes += ( `(gene_expression.gene.display_gene_id =\'${x}\') OR `));
+    geneList.forEach(x => genes += ( `(LOWER(gene_expression.gene.display_gene_id) = LOWER(\'${x}\')) OR `));
     return genes.substring(0, genes.length - 4);
 };
 
@@ -62,7 +62,7 @@ const buildExpressionQuery = function (query) {
 const listExpressionGeneData = function (gene, totalOutput) {
     let listOfData = [];
     totalOutput.forEach(function (x) {
-        if (x.display_gene_id === gene) {
+        if (x.display_gene_id.toLowerCase() === gene.toLowerCase()) {
             listOfData.push(Number(x.expression));
         }
     });

package/server/dals/grnsetting-dal.js

@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,

package/server/dals/network-dal.js

@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
@@ -21,12 +21,10 @@ const buildNetworkSourceQuery = function () {
     return "SELECT * FROM gene_regulatory_network.source ORDER BY time_stamp DESC;";
 };
 
-const buildNetworkGeneFromSourceQuery = function (gene, source, timestamp) {
+const buildNetworkGeneFromSourceQuery = function (gene) {
     return `SELECT DISTINCT gene_id, display_gene_id FROM 
-    gene_regulatory_network.network, gene_regulatory_network.gene WHERE
-    network.time_stamp='${timestamp}' AND network.source='${source}' AND
-    (gene.gene_id ='${gene}' OR gene.display_gene_id ='${gene}') AND
-    (gene.gene_id = network.regulator_gene_id OR gene.gene_id = network.target_gene_id);`;
+    gene_regulatory_network.gene WHERE (gene.gene_id ='${gene}'
+    OR gene.display_gene_id ='${gene}')`;
 };
 
 const buildNetworkGenesQuery = function (geneString) {
@@ -49,7 +47,7 @@ const buildGenerateNetworkQuery = function (genes, source, timestamp) {
 const buildQueryByType = function (queryType, query) {
     const networkQueries = {
         "NetworkSource": () => buildNetworkSourceQuery(),
-        "NetworkGeneFromSource": () => buildNetworkGeneFromSourceQuery(query.gene, query.source, query.timestamp),
+        "NetworkGeneFromSource": () => buildNetworkGeneFromSourceQuery(query.gene),
         "GenerateNetwork": () => buildGenerateNetworkQuery(query.genes, query.source, query.timestamp)
     };
     if (Object.keys(networkQueries).includes(query.type)) {

package/server/dals/protein-dal.js

@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,

package/test/additional-sheet-parser-tests.js

@@ -62,7 +62,7 @@ describe("additional-sheet-parser", function () {
             var data = parseAdditionalSheets(workbook);
             /* eslint-disable */
             assert(data.meta, {
-                alpha: 0.002,
+                alpha: 0.02,
                 kk_max: 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,

package/test/import-sif-tests.js

@@ -316,6 +316,13 @@ var sifWithSemanticErrorOnly = [
     "E"
 ].join("\r\n");
 
+var sifWithMixedRelationshipTypes = [
+    [ "A", "pd", "A" ].join("\t"),
+    [ "B", "pd", "A", "C" ].join("\t"),
+    [ "C", "pd", "B" ].join("\t"),
+    [ "D", "pp", "D" ].join("\t"),
+].join("\r\n");
+
 describe("Import from SIF", function () {
     it("should import unweighted workbooks from SIF correctly", function () {
         expect(
@@ -514,4 +521,10 @@ describe("Import from SIF syntactic checker", function () {
         ).to.deep.equal(expectedUnweightedGRNWorkbook);
     });
 
+    it("should throw an error for SIF files with mixed relationship types", function () {
+        expect(
+            importController.sifToGrnsight(sifWithMixedRelationshipTypes).errors[0].errorCode
+        ).to.equal("SIF_MIXED_RELATIONSHIP_TYPE_ERROR");
+    });
+
 });

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

@@ -55,6 +55,7 @@ export const MIN_EDGE_WEIGHT_NORMALIZATION      = 0.0001;
 export const MAX_EDGE_WEIGHT_NORMALIZATION      = 1000;
 
 export const DEFAULT_ZOOM_VALUE                 = 100;
+export const BOUNDARY_MARGIN                    = 5;
 
 export const GREY_EDGE_THRESHOLD_MENU           = "#gray-edge-threshold-menu";
 export const GREY_EDGE_THRESHOLD_SLIDER_SIDEBAR = "#grayThresholdInput";

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

@@ -1,8 +1,13 @@
 import Grid from "d3-v4-grid";
 import { grnState } from "./grnstate";
-import { modifyChargeParameter, modifyLinkDistanceParameter, valueValidator } from "./update-app";
 import {
-    ENDS_IN_EXPRESSION_REGEXP,
+    modifyChargeParameter,
+    modifyLinkDistanceParameter,
+    valueValidator,
+    adjustGeneNameForExpression,
+    hasExpressionData,
+} from "./update-app";
+import {
     VIEWPORT_FIT,
     ZOOM_INPUT,
     ZOOM_PERCENT,
@@ -11,7 +16,8 @@ import {
     ZOOM_DISPLAY_MAXIMUM_VALUE,
     ZOOM_DISPLAY_MIDDLE,
     ZOOM_ADAPTIVE_MAX_SCALE,
-    NETWORK_GRN_MODE
+    NETWORK_GRN_MODE,
+    BOUNDARY_MARGIN
 } from "./constants";
 
 /* globals d3 */
@@ -456,8 +462,6 @@ export var drawGraph = function (workbook) {
             center();
         }
         updateAppBasedOnZoomValue(); // Update zoom value within bounds
-        // Refresh the graph so that nodes and paths are adjusted to fit in viewport
-        tick();
     };
 
     d3.select("#restrict-graph-to-viewport").on("click", function () {
@@ -1087,20 +1091,20 @@ export var drawGraph = function (workbook) {
                 .selectAll(".coloring")
                 .data(function () {
                     if (grnState.workbook.expression[dataset]) {
+                        const geneName = adjustGeneNameForExpression(p);
                         if (
-                            grnState.workbook.expression[dataset].data[p.name]
+                            grnState.workbook.expression[dataset].data[geneName]
                         ) {
                             const result = getExpressionData(
-                                p.name,
+                                geneName,
                                 dataset,
                                 average
                             );
                             timePoints = result.timePoints;
-                            return result.data;
-                        } else {
-                            return 0;
+                            return result.data || [];
                         }
                     }
+                    return [];
                 })
                 .attr("class", "coloring")
                 .enter().append("rect")
@@ -1118,6 +1122,9 @@ export var drawGraph = function (workbook) {
                 .attr("stroke-width", "0px")
                 .style("fill", function (d) {
                     d = d || 0; // missing values are changed to 0
+                    if (d === 0) {
+                        return "white";
+                    }
                     var scale = d3.scaleLinear()
                         .domain([-logFoldChangeMaxValue, logFoldChangeMaxValue])
                         .range([0, 1]);
@@ -1227,15 +1234,6 @@ export var drawGraph = function (workbook) {
         }
     };
 
-    const hasExpressionData = sheets => {
-        for (var property in sheets) {
-            if (property.match(ENDS_IN_EXPRESSION_REGEXP)) {
-                return true;
-            }
-        }
-        return false;
-    };
-
     if (!$.isEmptyObject(workbook.expression) && hasExpressionData(workbook.expression) &&
       grnState.nodeColoring.topDataset !== undefined) {
         updaters.renderNodeColoring();
@@ -1383,8 +1381,6 @@ export var drawGraph = function (workbook) {
         }
     };
 
-    const BOUNDARY_MARGIN = 5;
-
     function viewportBoundsMoveDrag (graphZoom, dx, dy) {
         updateZoomContainerInfo();
         flexibleContainer = calcFlexiBox();
@@ -1526,7 +1522,6 @@ export var drawGraph = function (workbook) {
         try {
             node.attr("x", function (d) {
                 var selfReferringEdge = getSelfReferringEdge(d);
-
                 var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) +
                     selfReferringEdge.strokeWidth + 2 : 0);
                 var rightBoundary = width - (d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth;
@@ -1541,9 +1536,7 @@ export var drawGraph = function (workbook) {
                 }
                 // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds
                 var currentXPos = Math.max(getLeftXBoundaryMargin(), Math.min(rightBoundary, d.x));
-                if (
-                  adaptive &&
-                  width < MAX_WIDTH &&
+                if (adaptive && width < MAX_WIDTH &&
                   (currentXPos === getLeftXBoundaryMargin() ||
                     currentXPos === rightBoundary)
                 ) {

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

@@ -85,6 +85,7 @@ export const grnState = {
         lastDataset: null,
         bottomDataSameAsTop: true,
         nodeColoringOptions: [],
+        ppiNodeColorWarningDisplayed: false,
     },
 
 

package/web-client/public/js/setup-handlers.js

@@ -94,13 +94,11 @@ export const setupHandlers = grnState => {
         window.document.body.appendChild(emptySvg);
         var emptySvgDeclarationComputed = getComputedStyle(emptySvg);
 
-        const traverse = svg => {
-            var tree = [];
-            tree.push(svg);
-            // implement DFS
-            const visit = (node) => {
-                if (node && node.hasChildNodes()) {
-                    var child = node.firstChild;
+        const traverse = (node) => {
+            const tree = [];
+            const visit = (currentNode) => {
+                if (currentNode && currentNode.hasChildNodes()) {
+                    let child = currentNode.firstChild;
                     while (child) {
                         if (child.nodeType === 1 && child.nodeName !== "SCRIPT") {
                             tree.push(child);
@@ -110,38 +108,39 @@ export const setupHandlers = grnState => {
                     }
                 }
             };
-            visit(svg);
+            visit(node);
             return tree;
         };
 
         const explicitlySetStyle = element => {
-            const cSSStyleDeclarationComputed = window.getComputedStyle(element);
-            let i;
-            let len;
-            let key;
-            let value;
-            let computedStyleStr = "";
-
-            for (i = 0, len = cSSStyleDeclarationComputed.length; i < len; i++) {
-                key = cSSStyleDeclarationComputed[i];
-                value = cSSStyleDeclarationComputed.getPropertyValue(key);
+            const cssStyleDeclarationComputed = window.getComputedStyle(element);
+            const computedStyleObj = {};
+
+
+            for (let i = 0; i < cssStyleDeclarationComputed.length; i++) {
+                const key = cssStyleDeclarationComputed[i];
+                const value = cssStyleDeclarationComputed.getPropertyValue(key);
                 if (value !== emptySvgDeclarationComputed.getPropertyValue(key)) {
                     // Don't set computed style of width and height. Makes SVG elmements disappear.
                     if ((key !== "height") && (key !== "width")) {
-                        computedStyleStr += key + ":" + value + ";";
+                        computedStyleObj[key] = value;
                     }
 
                 }
             }
-            element.setAttribute("style", computedStyleStr);
+
+            if (element.classList.contains("weight")) {
+                computedStyleObj["visibility"] = "hidden";
+            }
+
+            if (computedStyleObj) {
+                Object.assign(element.style, computedStyleObj);
+            }
         };
 
         // hardcode computed css styles inside svg
         var allElements = traverse(svg);
-        var i = allElements.length;
-        while (i--) {
-            explicitlySetStyle(allElements[i]);
-        }
+        allElements.forEach(explicitlySetStyle);
     };
 
     const sourceAttributeSetter = (svg) => {
@@ -160,7 +159,7 @@ export const setupHandlers = grnState => {
     };
 
     const exportSVG = (svgElement, name) => {
-        let source = svgElement;
+        let source = svgElement.cloneNode(true);
 
         sourceAttributeSetter(source);
         setInlineStyles(source);
@@ -185,10 +184,30 @@ export const setupHandlers = grnState => {
         const imgData = canvas.toDataURL("image/png");
 
         const pdf = new jsPDF("l", "mm", "letter");
-        const width = pdf.internal.pageSize.getWidth();
-        const height = pdf.internal.pageSize.getHeight();
+        const pdfWidth = pdf.internal.pageSize.getWidth();
+        const pdfHeight = pdf.internal.pageSize.getHeight();
+
+        const svgWidth = canvas.width;
+        const svgHeight = canvas.height;
+
+        const aspectRatio = svgWidth / svgHeight;
+        let scaledWidth = pdfWidth;
+        // ratio = width/height --> height = width/ratio
+        let scaledHeight = scaledWidth / aspectRatio;
+
+        if (scaledHeight > pdfHeight) {
+            scaledHeight = pdfHeight;
+            scaledWidth = pdfHeight * aspectRatio;
+        }
 
-        pdf.addImage(imgData, "PNG", 0, 0, width, height);
+        pdf.addImage(
+            imgData,
+            "PNG",
+            (pdfWidth - scaledWidth) / 2,
+            (pdfHeight - scaledHeight) / 2,
+            scaledWidth,
+            scaledHeight
+        );
         pdf.save(name);
     };
 
@@ -209,7 +228,7 @@ export const setupHandlers = grnState => {
     $(EXPORT_TO_PNG).click(() => {
         var svgContainer = document.getElementById("exportContainer");
         var editedName = grnState.name.replace(determineFileType(grnState.name), "") + ".png";
-        saveSvgAsPng(svgContainer, editedName);
+        saveSvgAsPng(svgContainer, editedName, { backgroundColor: "white"});
     });
 
     $(EXPORT_TO_SVG).click(() => {

package/web-client/public/js/setup-load-and-import-handlers.js

@@ -171,8 +171,8 @@ export const setupLoadAndImportHandlers = (grnState) => {
      * for helping to resolve this.
      */
 
-    // $(".upload").change(uploadHandler(loadGrn));
     $("body").on("change", ".upload", uploadHandler(loadGrn));
+
     const loadDemo = (url, value) => {
         $("#demoSourceDropdown option[value='" + value.substring(1) + "']").prop(
             "selected",

package/web-client/public/js/update-app.js

@@ -1,6 +1,6 @@
 import { drawGraph, updaters } from "./graph";
 import { uploadState } from "./upload";
-import { displayWarnings } from "./warnings";
+import { displayWarnings, displayPPINodeColorWarning } from "./warnings";
 import { max } from "d3-array";
 import { grnState } from "./grnstate";
 
@@ -109,7 +109,7 @@ import {
   NETWORK_MODE_GRN,
   EXPORT_TO_UNWEIGHTED_GML_MENU,
   NETWORK_GRN_MODE,
-  NETWORK_PPI_MODE
+  NETWORK_PPI_MODE,
 //   EXPRESSION_SOURCE,
 } from "./constants";
 
@@ -384,6 +384,14 @@ const enableNodeColoringUI = function () {
     $(LOG_FOLD_CHANGE_MAX_VALUE_HEADER).removeClass("hidden");
 };
 
+const adjustGeneNameForExpression = function (gene) {
+    const geneName = gene.name;
+    return grnState.workbook.meta.data.workbookType === NETWORK_PPI_MODE &&
+        geneName.endsWith("p")
+        ? geneName.slice(0, -1)
+        : geneName;
+};
+
 const loadExpressionDatabase = function (isTopDataset) {
     const dataset = isTopDataset ? grnState.nodeColoring.topDataset : grnState.nodeColoring.bottomDataset;
     startLoadingIcon();
@@ -394,7 +402,9 @@ const loadExpressionDatabase = function (isTopDataset) {
         queryExpressionDatabase({
             type:"ExpressionData",
             dataset,
-            genes : grnState.workbook.genes.map(gene => {return gene.name;}).join(","),
+            genes: grnState.workbook.genes
+                    .map(adjustGeneNameForExpression)
+                    .join(","),
             timepoints: timepointsResponse[dataset]
         }).then(function (response) {
             if (isTopDataset) {
@@ -502,6 +512,10 @@ const toggleLayout = (on, off) => {
     }
 };
 
+export const hasExpressionData = (sheets) => {
+    return Object.keys(sheets).some(property => property.match(ENDS_IN_EXPRESSION_REGEXP));
+};
+
 const updatetoForceGraph = () => {};
 
 const updatetoGridLayout = () => {};
@@ -528,7 +542,6 @@ const isNewWorkbook = (name) => {
 };
 
 // Workbook Mode Functions
-
 const updateModeViews = () =>{
     // Select correct dropdown item
     $(`${NETWORK_MODE_DROPDOWN} option`).removeAttr("selected");
@@ -543,14 +556,18 @@ const updateModeViews = () =>{
 };
 
 const checkWorkbookModeSettings = () => {
-    if (grnState.mode === NETWORK_PPI_MODE) {
+    const hasExpression = hasExpressionData(grnState.workbook.expression);
+
+    if (grnState.mode === NETWORK_PPI_MODE || !hasExpression) {
         grnState.nodeColoring.nodeColoringEnabled = false;
+        grnState.nodeColoring.showMenu = true;
         grnState.colorOptimal = false;
-        disableNodeColoringMenus();
+        showNodeColoringMenus();
         hideEdgeWeightOptions();
         updateModeViews();
     } else if (grnState.mode === NETWORK_GRN_MODE) {
         grnState.nodeColoring.nodeColoringEnabled = true;
+        grnState.nodeColoring.showMenu = true;
         grnState.colorOptimal = true;
         showNodeColoringMenus();
         showEdgeWeightOptions();
@@ -587,15 +604,6 @@ const shortenExpressionSheetName = (name) => {
       (name.slice(0, MAX_NUM_CHARACTERS_DROPDOWN) + "...") : name;
 };
 
-const hasExpressionData = (sheets) => {
-    for (var property in sheets) {
-        if (property.match(ENDS_IN_EXPRESSION_REGEXP)) {
-            return true;
-        }
-    }
-    return false;
-};
-
 const updateSpeciesMenu = () => {
     $(SPECIES_DISPLAY).val(grnState.genePageData.species);
     $(SPECIES_BUTTON_CRESS + " span").removeClass("glyphicon-ok");
@@ -878,6 +886,10 @@ export const updateApp = grnState => {
         $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden");
         $(NODE_COLORING_MENU).removeClass("hidden");
         $(NODE_COLORING_NAVBAR_OPTIONS).removeClass("hidden");
+        if (grnState.mode === NETWORK_PPI_MODE) {
+            displayPPINodeColorWarning(grnState.ppiNodeColorWarningDisplayed);
+            grnState.ppiNodeColorWarningDisplayed = true;
+        }
         if (grnState.database.expressionDatasets.includes(grnState.nodeColoring.topDataset) &&
         grnState.workbook.expression[grnState.nodeColoring.topDataset] === undefined) {
             if ($(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked")) {
@@ -905,6 +917,12 @@ export const updateApp = grnState => {
         grnState.nodeColoring.topDataset : "Dahlquist_2018_wt";
         grnState.nodeColoring.bottomDataset = grnState.nodeColoring.bottomDataset ?
         grnState.nodeColoring.bottomDataset : "Dahlquist_2018_wt";
+        $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", true);
+        $(`${NODE_COLORING_TOGGLE_MENU} span`).addClass("glyphicon-ok");
+        $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden");
+        $(NODE_COLORING_MENU).removeClass("hidden");
+        $(NODE_COLORING_NAVBAR_OPTIONS).removeClass("hidden");
+        $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(DEFAULT_MAX_LOG_FOLD_CHANGE);
         $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).addClass("hidden");
         $(LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_BUTTON).addClass("hidden");
         $(LOG_FOLD_CHANGE_MAX_VALUE_HEADER).addClass("hidden");
@@ -931,7 +949,10 @@ export const updateApp = grnState => {
                 //   Investigate why a timeout is required in order for node coloring to take place
                 //   successfully in this case.
                 setTimeout(() => updaters.renderNodeColoring(), 250);
-
+            }
+            if (grnState.mode === NETWORK_PPI_MODE) {
+                displayPPINodeColorWarning(grnState.ppiNodeColorWarningDisplayed);
+                grnState.ppiNodeColorWarningDisplayed = true;
             }
         }
     } else if (grnState.workbook !== null && !grnState.nodeColoring.nodeColoringEnabled) {
@@ -940,6 +961,9 @@ export const updateApp = grnState => {
         $(NODE_COLORING_NAVBAR_OPTIONS).addClass("hidden");
         $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok");
         $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", false);
+        if (grnState.mode === NETWORK_PPI_MODE) {
+            grnState.ppiNodeColorWarningDisplayed = false;
+        }
     }
 
     if (grnState.workbook !== null &&  grnState.workbook.sheetType === "weighted") {
@@ -1010,4 +1034,4 @@ export const updateApp = grnState => {
 };
 
 
-export { stopLoadingIcon, startLoadingIcon};
+export { stopLoadingIcon, startLoadingIcon, adjustGeneNameForExpression};

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

@@ -120,7 +120,7 @@ export const upload = function () {
     const updateOptimizationParameters = (finalExportSheets) => {
         let optimizationParameters = {
             data: grnState.mode === NETWORK_GRN_MODE ? {
-                alpha: 0.002,
+                alpha: 0.02,
                 "kk_max": 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
@@ -261,7 +261,7 @@ export const upload = function () {
             } else if (sheet === "network") {
                 finalExportSheets.networks[sheet] = grnState.workbook.network;
             } else if (sheet === "network_weights") {
-                finalExportSheets.networks[sheet] = grnState.workbook.networkWeights;
+                finalExportSheets.networks[sheet] = grnState.workbook.network; // network_weights is identical to network
             } else if (sheet === "optimization_diagnostics") { // Get the additional Sheets
                 finalExportSheets[sheet] = grnState.workbook.meta2;
             } else if (sheet === "optimization_parameters") {
@@ -430,7 +430,7 @@ export const upload = function () {
         let networks = [
             [grnState.workbook.network !== undefined, "network"],
             [grnState.workbook.networkOptimizedWeights !== undefined, "network_optimized_weights"],
-            [grnState.workbook.networkWeights !== undefined, "network_weights"]];
+            [grnState.workbook.network !== undefined, "network_weights"]]; // network_weights is always available if network is available
         // networks = networks.filter(x => x !== false);
         let additionalsheets = grnState.workbook.twoColumnSheets ? [
             ...Object.keys(grnState.workbook.twoColumnSheets),

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

@@ -58,3 +58,28 @@ export var displayWarnings = function (warnings) {
 
     $("#warningsModal").modal("show");
 };
+
+export var displayPPINodeColorWarning = function (warningDisplayed) {
+    if (warningDisplayed) {
+        return;
+    }
+
+    $("#warningIntro").html("Protein-protein interaction node coloring warning.");
+    $("#warningsList").html(
+      ["You are displaying mRNA-level expression data on a protein-protein interaction network.",
+          "Please note that this may not be the most appropriate representation of the data."].join(" ")
+    );
+
+    var screenHeight = $(window).height();
+    var MIN_SCREEN_HEIGHT = 600;
+    var BORDER = 425;
+    var setPanel = screenHeight - BORDER + "px";
+    var minPanel = MIN_SCREEN_HEIGHT - BORDER + "px";
+    if (screenHeight > MIN_SCREEN_HEIGHT) {
+        $("#list-frame").css({ height: setPanel });
+    } else {
+        $("#list-frame").css({ height: minPanel });
+    }
+
+    $("#warningsModal").modal("show");
+};

package/web-client/views/upload.pug

@@ -513,7 +513,7 @@ html
             p(id='error')
           div(class='modal-footer')
             input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
-            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('.upload').click()")
+            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload-network').click()")
 
     div(id='warningsModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')