grnsight 6.0.7 → 7.2.0

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

@@ -12,6 +12,7 @@ import {
 } from "./update-app";
 
 import { queryExpressionDatabase } from "./api/grnsight-api.js";
+import { NETWORK_PPI_MODE, NETWORK_GRN_MODE } from "./constants.js";
 
 
 const EXPRESSION_SHEET_SUFFIXES = ["_expression", "_optimized_expression", "_sigmas"];
@@ -118,8 +119,8 @@ export const upload = function () {
 
     const updateOptimizationParameters = (finalExportSheets) => {
         let optimizationParameters = {
-            data: {
-                alpha: 0.002,
+            data: grnState.mode === NETWORK_GRN_MODE ? {
+                alpha: 0.02,
                 "kk_max": 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
@@ -131,29 +132,69 @@ export const upload = function () {
                 "make_graphs": 1,
                 "fix_P": 0,
                 "fix_b": 0,
+                species: "Saccharomyces cerevisiae",
+                "taxon_id":559292,
+                workbookType: NETWORK_GRN_MODE
+            } : {
+                species: "Saccharomyces cerevisiae",
+                "taxon_id":559292,
+                workbookType: NETWORK_PPI_MODE
             }
         };
-        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;
+        if (grnState.mode === NETWORK_GRN_MODE) {
+            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;
     };
 
+    // helper method for handleExpressionDataAndExport to reduce indentation
+    const expressionDataHandler = (expressionData, sheet, route, extension, sheetType, finalExportSheets) => {
+        finalExportSheets.expression[sheet] = expressionData;
+        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);
+            }
+        }
+    };
+
+    // helper method for handleExpressionDataAndExport and handleExportExcelButtonExport to avoid redundant code
+    const expressionExportErrorHandler = (error) => {
+        console.log(error.stack);
+        console.log(error.name);
+        console.log(error.message);
+    };
+
     const handleExpressionDataAndExport = (route, extension, sheetType, source, finalExportSheets) => {
         if (source === "userInput" && grnState.workbook.expression) {
             // make sure that the optimization parameters sheet is actually properly formatted
@@ -178,42 +219,13 @@ export const upload = function () {
                             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);
-                });
+                    }).then((expressionData) => expressionDataHandler(expressionData, sheet, route, extension, sheetType, finalExportSheets))
+                    .catch((error) => expressionExportErrorHandler(error));
+                }).catch((error) => expressionExportErrorHandler(error));
             }
         }
     };
 
-
     const handleExportExcelButtonExport = (route, extension, sheetType, source) => {
         grnState.workbook.exportNetworkType = sheetType;
         const workbookSheets = $("input[name=workbookSheets]:checked");
@@ -249,7 +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") {
@@ -296,23 +308,27 @@ export const upload = function () {
 
                     queryExpressionDatabase({
                         type: twoColumnSheetType[sheet],
-                        genes: grnState.workbook.genes.map(x => {
+                        genes: grnState.workbook.genes
+                        .map((x) => {
                             return x.name;
-                        }).join(",")
-                    }).then(function (response) {
+                        })
+                        .join(","),
+                    })
+                    .then(function (response) {
                         result.data = response;
                         finalExportSheets.two_column_sheets[sheet] = result;
-                        if (!Object.values(finalExportSheets.two_column_sheets).includes(null)) {
+                        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);
+                            handleExpressionDataAndExport(
+                                route,
+                                extension,
+                                sheetType,
+                                source,
+                                finalExportSheets
+                            );
                         }
-
-                    }).catch(function (error) {
-                        console.log(error.stack);
-                        console.log(error.name);
-                        console.log(error.message);
-                    });
-
+                    })
+                      .catch(error => expressionExportErrorHandler(error));
                 }
             }
         } else {
@@ -366,7 +382,7 @@ export const upload = function () {
         };
     };
 
-    const createHTMLforForm = () => {
+    const createHTMLforGRNForm = () => {
         const sources = [...new Set(grnState.database.expressionDatasets.map(s => s.slice(0, s.lastIndexOf("_"))))];
         let result = `
         <form id=\'exportExcelForm\'>
@@ -414,7 +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),
@@ -422,7 +438,7 @@ export const upload = function () {
         ] : [
             (grnState.workbook.meta2 !== undefined && "optimization_diagnostics")
         ];
-        additionalsheets = additionalsheets.filter(x => (x !== false && -1 !== optionalAdditionalSheets.indexOf(x)));
+        additionalsheets = additionalsheets.filter(sheet => (sheet && -1 !== optionalAdditionalSheets.indexOf(sheet)));
         additionalsheets = [...optionalAdditionalSheets, ...additionalsheets].sort();
         additionalsheets = [...(new Set(additionalsheets))];
         for (let n of networks) {
@@ -506,6 +522,34 @@ export const upload = function () {
         `;
     };
 
+    const createHTMLforProteinProteinPhysicalInteractionForm = () => {
+        $(".export-excel-workbook-sheet-option").remove();
+        // check if user updated data is selected
+        let result = `
+            <form id=\'exportExcelForm\'>
+                <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;\">
+                        <p class=\'export-excel-workbook-sheet-option-subheader\'> Network Sheets </p>
+                        <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>
+                        <p class=\'export-excel-workbook-sheet-option-subheader\'> Additional Sheets </p>
+                        <li class=\'export-excel-workbook-sheet-option\'>
+                            <input type=\'checkbox\' name=\'workbookSheets\' checked=\"true\" value=\"optimization_parameters\" id=\'exportExcelWorkbookSheet-optimization_parameters\' class=\'export-checkbox\' />
+                            <label for=\'exportExcelWorkbookSheet-optimization_parameters\' id=\'exportExcelWorkbookSheet-optimization_parameters-label\' class=\'export-checkbox-label\' >
+                                optimization_parameters
+                            </label>
+                        </li>
+                    </ul>
+                </div>
+            </form>`;
+        return result;
+    };
+
 
     var handleWorkbookSheetCheckboxBehaviour = () => {
         $("input[name=workbookSheets]").not($("#exportExcelWorkbookSheet-All")).on("click", () => {
@@ -538,24 +582,37 @@ export const upload = function () {
         $("#Export-Excel-Button").on("click", performExport("export-to-excel", "xlsx", null, source));
     };
     const handleExportExcelModal = function () {
-        $("#exportExcelForm").remove();
-        $("#exportExcelFooter").remove();
-        $("#exportExcelQuestions-containter").append(createHTMLforForm);
-        $("#exportExcelFooter-container").append(createHTMLforModalButtons());
-        $("#Export-Excel-Button").prop("value", "Export Workbook");
-        $("#exportExcelExpressionSources").html("Select the Expression Data Source:");
-        $("#exportExcelExpressionSource-userInput").html(grnState.name);
-        $("#exportExcelWorkbookSheets").html("Select Workbook Sheets to Export:");
-        let source = $("input[name=expressionSource]:checked")[0].value;
-        $("#exportExcelForm").on("change", function () {
-            const selectedValue = $("input[name=expressionSource]:checked")[0].value;
-            if (selectedValue !== source) {
-                source = selectedValue;
-                $(".export-excel-workbook-sheet-option-subheader").remove();
-                handleExpressionSheetsFromSource(source);
-            }
-        });
-        handleExpressionSheetsFromSource(source);
+        if (grnState.mode === NETWORK_GRN_MODE) {
+            $("#exportExcelForm").remove();
+            $("#exportExcelFooter").remove();
+            $("#exportExcelQuestions-containter").append(createHTMLforGRNForm);
+            $("#exportExcelFooter-container").append(createHTMLforModalButtons());
+            $("#Export-Excel-Button").prop("value", "Export Workbook");
+            $("#exportExcelExpressionSources").html("Select the Expression Data Source:");
+            $("#exportExcelExpressionSource-userInput").html(grnState.name);
+            $("#exportExcelWorkbookSheets").html("Select Workbook Sheets to Export:");
+            let source = $("input[name=expressionSource]:checked")[0].value;
+            $("#exportExcelForm").on("change", function () {
+                const selectedValue = $("input[name=expressionSource]:checked")[0].value;
+                if (selectedValue !== source) {
+                    source = selectedValue;
+                    $(".export-excel-workbook-sheet-option-subheader").remove();
+                    handleExpressionSheetsFromSource(source);
+                }
+            });
+            handleExpressionSheetsFromSource(source);
+        } else if (grnState.mode === NETWORK_PPI_MODE) {
+            const source = "userInput";
+            $("#exportExcelForm").remove();
+            $("#exportExcelFooter").remove();
+            $("#exportExcelQuestions-containter").append(createHTMLforProteinProteinPhysicalInteractionForm);
+            $("#exportExcelFooter-container").append(createHTMLforModalButtons());
+            $("#Export-Excel-Button").prop("value", "Export Workbook");
+            $("#exportExcelWorkbookSheets").html("Select Workbook Sheets to Export:");
+            handleWorkbookSheetCheckboxBehaviour();
+            $("#Export-Excel-Button").on("click", performExport("export-to-excel", "xlsx", null, source));
+
+        }
     };
 
 

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/public/lib/bootstrap.file-input/bootstrap.file-input.js

@@ -84,7 +84,6 @@ $.fn.bootstrapFileInput = function() {
     });
 
     $('body').on('change', '.file-input-wrapper input[type=file]', function(){
-
       var fileName;
       fileName = $(this).val();
 

package/web-client/public/stylesheets/grnsight.styl

@@ -100,12 +100,6 @@ form label, form span
   top: 1px
   margin-right: auto
   margin-bottom: 10px
-
-.glyphicon
-  min-width: 22px
-
-.glyphicon-searchbar
-  margin-left: -22px
   
 .dropdown-menu > li > a.upload
   padding-top: 7px
@@ -169,8 +163,9 @@ nav.navbar.navbar-default
   font-size: 12px
   display: inline-block
 
-.dropdown-menu > li > a:hover
+.dropdown-menu > li > a:hover, .dropdown-menu > #node-coloring-navbar-options > li > a:hover
   background-color: #dfebe5
+  text-decoration: none;
 
 #undoResetButton
   margin-top: 5px
@@ -252,7 +247,7 @@ nav.navbar.navbar-default
 .dropdown-submenu
     position:relative
 
-.dropdown-submenu>.dropdown-menu
+.dropdown-submenu>.dropdown-menu, .dropdown-menu > #node-coloring-navbar-options dropdown-submenu
     top:0
     left:100%
     margin-top:-6px
@@ -261,9 +256,12 @@ nav.navbar.navbar-default
     -moz-border-radius:0 6px 6px 6px
     border-radius:0 6px 6px 6px
 
-.dropdown-submenu:hover>.dropdown-menu
+.dropdown-submenu:hover>.dropdown-menu, #node-coloring-navbar-options .dropdown-submenu:hover>.dropdown-menu
     display:block
 
+#node-coloring-navbar-options .disabled:hover>.dropdown-menu
+    display:none
+
 .dropdown-submenu>a:after
     display:block
     content:" "
@@ -280,22 +278,43 @@ nav.navbar.navbar-default
 .dropdown-submenu:hover>a:after
     border-left-color:#ffffff
 
-.dropdown-submenu.pull-left
+#node-coloring-navbar-options>li>a
+    display: block;
+    padding: 3px 20px;
+    clear: both;
+    font-weight: 400;
+    line-height: 1.42857143;
+    color: #333;
+    white-space: nowrap;
+
+#node-coloring-navbar-options>.disabled>a, #node-coloring-navbar-options
+    color: #999;
+    cursor: not-allowed;
+    text-decoration: none;
+    aria-disabled: true;
+
+.dropdown-menu > #node-coloring-navbar-options > .disabled > a:hover
+    background-color: #FFFFFF;
+
+.dropdown-submenu.pull-left, #node-coloring-navbar-options .dropdown-submenu.pull-left
     float:none
 
-.dropdown-submenu.pull-left>.dropdown-menu
+#node-coloring-navbar-options
+    cursor: pointer
+
+.dropdown-submenu.pull-left>.dropdown-menu, .dropdown-submenu.pull-left, .dropdown-menu #node-coloring-navbar-options .dropdown-submenu.pull-left
     left:-100%
     margin-left:10px
     -webkit-border-radius:6px 0 6px 6px
     -moz-border-radius:6px 0 6px 6px
     border-radius:6px 0 6px 6px
 
-.dropdown a.with-input
+.dropdown a.with-input, #node-coloring-navbar-options a.with-input
     display:flex
     align-items:center
     user-select:none
 
-.dropdown a.with-input>*:last-child
+.dropdown a.with-input>*:last-child, #node-coloring-navbar-options a.with-input > *:last-child
     margin-left:auto
 
 // Graph statistics styling is due to absolute position and size of grnsight-container
@@ -471,7 +490,8 @@ path.mousezone
 
 #Saccharomyces-cerevisiae
   color: #AAA
-  margin-left: 30px
+  margin-left: 20px
+
 
 .create-network-label
   font-weight: normal
@@ -522,7 +542,8 @@ path.mousezone
   background-color: #81ecec
   border: 2px solid #00cec9
 
-
+.glyphicon
+  min-width: 22px
 
 .sidebar-glyphicon
   margin-right: 0px
@@ -536,6 +557,7 @@ path.mousezone
 #enter-search
   margin-left: 0px
   height: 100%
+  margin-bottom: 2px
   padding: 0
   border-color:#aeaeae
 
@@ -603,10 +625,12 @@ path.mousezone
 # demoSourceDropdown > option { 
   direction: ltr; 
   }
+# networkModeDropdown > option {
+  font-size: 14px
+}
 
 .panelDropdownContainer > select {
   right: auto;
-  padding: 13px 45px 15px 0px;
   direction: ltr;
 }
 

package/web-client/views/components/demo.pug

@@ -1,10 +1,12 @@
-ul(class='dropdown-menu' role='menu')
+ul(class='dropdown-menu' role='menu' id="demo-dropdown")
   li
-    a(href='#' class='unweighted') Demo #1: Unweighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
+    a(href='#' class='unweighted' data-expression="unweighted") Demo #1: Unweighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
   li
-    a(href='#' class='weighted') Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
+    a(href='#' class='weighted' data-expression="weighted") Demo #2: Weighted GRN (15 genes, 28 edges, Dahlquist Lab unpublished data)
   li
-    a(href='#' class='schadeInput') Demo #3: Unweighted GRN (21 genes, 31 edges)
+    a(href='#' class='schadeInput' data-expression="schadeInput") Demo #3: Unweighted GRN (21 genes, 31 edges)
   li
-    a(href='#' class='schadeOutput') Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data)
+    a(href='#' class='schadeOutput' data-expression="schadeOutput") Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data)
+  li
+    a(href='#' class='ppi' data-expression="ppi") Demo #5: PPI (18 proteins, 81 edges)