grnsight 6.0.4 → 7.1.1

package/server/controllers/demo-workbooks.js

@@ -1,3 +1,5 @@
+const constants = require("./constants");
+
 /* eslint-disable camelcase */
 var helpers = require(__dirname + "/helpers");
 
@@ -529,7 +531,8 @@ var demoWorkbook1 = function (path, res, app) {
                 Strain: ["wt", "dcin5", "dgln3", "dhap4", "dhmo1", "dzap1"],
                 simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60],
                 species: "Saccharomyces cerevisiae",
-                taxon_id: 559292
+                taxon_id: 559292,
+                workbookType: constants.NETWORK_GRN_MODE
             }
         },
         twoColumnSheets: {
@@ -2692,7 +2695,8 @@ var demoWorkbook2 = function (path, res, app) {
                 Strain: ["wt", "dcin5", "dgln3", "dhap4", "dhmo1", "dzap1"],
                 simulation_timepoints: [0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60],
                 species: "Saccharomyces cerevisiae",
-                taxon_id: 559292
+                taxon_id: 559292,
+                workbookType: constants.NETWORK_GRN_MODE
             }
         },
         twoColumnSheets: {
@@ -4619,7 +4623,8 @@ var demoWorkbook3 = function (path, res, app) {
                 MaxFunEval: 1000000,
                 TolX: 0.00001,
                 species: "Saccharomyces cerevisiae",
-                taxon_id: 559292
+                taxon_id: 559292,
+                workbookType: constants.NETWORK_GRN_MODE
             }
         },
         twoColumnSheets: {},
@@ -5680,7 +5685,8 @@ var demoWorkbook4 = function (path, res, app) {
                 MaxFunEval: 1000000,
                 TolX: 0.00001,
                 species: "Saccharomyces cerevisiae",
-                taxon_id: 559292
+                taxon_id: 559292,
+                workbookType: constants.NETWORK_GRN_MODE
             }
         },
         twoColumnSheets: {},
@@ -5960,6 +5966,1454 @@ var demoWorkbook4 = function (path, res, app) {
     return processDemo(path, res, app, workbook4);
 };
 
+var demoWorkbook5 = function (path, res, app) {
+    let workbook5 = {
+        genes: [
+            {
+                name: "Aim32p",
+            },
+            {
+                name: "Ccr4p",
+            },
+            {
+                name: "Erv1p",
+            },
+            {
+                name: "Fbp1p",
+            },
+            {
+                name: "Hsc82p",
+            },
+            {
+                name: "Hsp78p",
+            },
+            {
+                name: "Mia40p",
+            },
+            {
+                name: "Mpt5p",
+            },
+            {
+                name: "Nab2p",
+            },
+            {
+                name: "Osm1p",
+            },
+            {
+                name: "Puf3p",
+            },
+            {
+                name: "Sod2p",
+            },
+            {
+                name: "Srp54p",
+            },
+            {
+                name: "Ssc1p",
+            },
+            {
+                name: "Tim17p",
+            },
+            {
+                name: "Tim22p",
+            },
+            {
+                name: "Tim23p",
+            },
+            {
+                name: "Tim50p",
+            },
+        ],
+        links: [
+            {
+                source: 0,
+                target: 1,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 1,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 2,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 2,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 3,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 3,
+                target: 3,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 3,
+                target: 4,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 4,
+                target: 4,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 5,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 5,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 4,
+                target: 5,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 6,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 6,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 6,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 6,
+                target: 6,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 7,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 7,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 4,
+                target: 7,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 7,
+                target: 7,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 4,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 5,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 6,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 7,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 8,
+                target: 8,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 9,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 9,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 4,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 5,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 6,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 8,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 10,
+                target: 10,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 11,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 8,
+                target: 11,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 11,
+                target: 11,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 12,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 4,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 5,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 6,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 7,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 8,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 10,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 11,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 13,
+                target: 13,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 6,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 7,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 8,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 10,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 13,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 14,
+                target: 14,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 15,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 15,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 6,
+                target: 15,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 10,
+                target: 15,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 1,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 2,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 5,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 10,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 11,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 13,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 14,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 15,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 16,
+                target: 16,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 0,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 5,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 10,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 13,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 14,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 16,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+            {
+                source: 17,
+                target: 17,
+                value: 1,
+                type: "arrowhead",
+                stroke: "black",
+            },
+        ],
+        errors: [],
+        warnings: [],
+        positiveWeights: [
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+            1,
+        ],
+        negativeWeights: [],
+        sheetType: "unweighted",
+        meta: {
+            data: {
+                workbookType: constants.NETWORK_PPI_MODE,
+                species: "Saccharomyces cerevisiae",
+                taxon_id: "559292",
+            },
+            errors: [],
+            warnings: [],
+        },
+        expression: {},
+        network: {
+            genes: [
+                {
+                    name: "Aim32p",
+                },
+                {
+                    name: "Ccr4p",
+                },
+                {
+                    name: "Erv1p",
+                },
+                {
+                    name: "Fbp1p",
+                },
+                {
+                    name: "Hsc82p",
+                },
+                {
+                    name: "Hsp78p",
+                },
+                {
+                    name: "Mia40p",
+                },
+                {
+                    name: "Mpt5p",
+                },
+                {
+                    name: "Nab2p",
+                },
+                {
+                    name: "Osm1p",
+                },
+                {
+                    name: "Puf3p",
+                },
+                {
+                    name: "Sod2p",
+                },
+                {
+                    name: "Srp54p",
+                },
+                {
+                    name: "Ssc1p",
+                },
+                {
+                    name: "Tim17p",
+                },
+                {
+                    name: "Tim22p",
+                },
+                {
+                    name: "Tim23p",
+                },
+                {
+                    name: "Tim50p",
+                },
+            ],
+            links: [
+                {
+                    source: 0,
+                    target: 1,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 1,
+                    target: 1,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 2,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 2,
+                    target: 2,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 3,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 3,
+                    target: 3,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 3,
+                    target: 4,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 4,
+                    target: 4,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 5,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 1,
+                    target: 5,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 4,
+                    target: 5,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 6,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 1,
+                    target: 6,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 2,
+                    target: 6,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 6,
+                    target: 6,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 7,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 1,
+                    target: 7,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 4,
+                    target: 7,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 7,
+                    target: 7,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 1,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 2,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 4,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 5,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 6,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 7,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 8,
+                    target: 8,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 9,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 2,
+                    target: 9,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 0,
+                    target: 10,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 1,
+                    target: 10,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
+                {
+                    source: 2,
+                    target: 10,
+                    value: 1,
+                    type: "arrowhead",
+                    stroke: "black",
+                },
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+    return processDemo(path, res, app, workbook5);
+};
+
 module.exports = function (path, res, app, workbook) {
     if (path === "test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx") {
         return demoWorkbook1(path, res, app, workbook);
@@ -5969,5 +7423,7 @@ module.exports = function (path, res, app, workbook) {
         return demoWorkbook3(path, res, app, workbook);
     } else if (path === "test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx") {
         return demoWorkbook4(path, res, app, workbook);
+    } else if (path === "test-files/demo-files/18_proteins_81_edges_PPI.xlsx") {
+        return demoWorkbook5(path, res, app, workbook);
     }
 };