grnsight 5.0.0 → 5.1.0

package/.travis.yml

@@ -1,6 +1,6 @@
 language: node_js
 node_js:
-  - "8"
+  - "10"
 script:
   - npm test
   - npm run lint

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "grnsight",
-  "version": "5.0.0",
+  "version": "5.1.0",
   "description": "Web app and service for visualizing models of gene regulatory networks",
   "directories": {
     "test": "test"
@@ -17,7 +17,6 @@
     "fs": "0.0.1-security",
     "googleapis": "1.1.5",
     "http": "0.0.0",
-    "jade": "1.11.0",
     "jspdf": "1.5.3",
     "method-override": "2.3.10",
     "moment": "2.24.0",
@@ -28,12 +27,13 @@
     "parallelshell": "3.0.1",
     "pg": "^8.0.0",
     "pg-hstore": "^2.3.3",
+    "pug": "^3.0.2",
     "querystring": "^0.2.0",
     "save-svg-as-png": "1.4.14",
     "sequelize": "^5.21.6",
     "serve-static": "1.13.1",
     "should": "11.2.0",
-    "stylus": "0.54.5",
+    "stylus": "^0.54.5",
     "supertest": "3.0.0",
     "url": "^0.11.0",
     "webpack": "4.0.0",
@@ -41,13 +41,13 @@
     "xmlbuilder": "8.2.2"
   },
   "devDependencies": {
-    "browser-env": "3.2.5",
+    "browser-env": "^3.3.0",
     "chai": "4.1.2",
     "coveralls": "2.13.1",
     "eslint": "3.19.0",
     "isomorphic-fetch": "2.2.1",
     "istanbul": "0.4.5",
-    "jquery": "3.4.1",
+    "jquery": "^3.6.0",
     "jquery-extend": "2.0.3",
     "jsdom": "11.11.0",
     "markdown-pdf": "8.0.0",

package/server/app.js

@@ -15,8 +15,10 @@ var app = express();
 app.set("port", process.env.PORT || config.port || 3000);
 app.use(morgan("dev"));
 app.use(express.json());
-app.use(bodyParser.urlencoded({extended: true}));
-app.use(bodyParser.json());
+// app.use(bodyParser.urlencoded({extended: true}));
+// app.use(bodyParser.json());
+app.use(bodyParser.json({limit: "50mb"}));
+app.use(bodyParser.urlencoded({limit: "50mb", extended: true}));
 app.use(methodOverride());
 app.use(cors());
 

package/server/controllers/database-controller.js

@@ -1,3 +1,4 @@
+
 const Sequelize = require("sequelize");
 require("dotenv").config();
 var env = process.env.NODE_ENV || "development";
@@ -64,30 +65,30 @@ timepointsSources.forEach(source => timepointsByDataset[source.key] = source.val
 
 let buildTimepointsQuery = function (selection) {
     let timepoints = "";
-    selection.forEach(x => timepoints += ("timepoints=\'" + x + "\' OR "));
+    selection.forEach(x => timepoints += ("fall2021.expression.time_point=" + x + " OR "));
     return timepoints.substring(0, timepoints.length - 4);
 };
 
 let buildGenesQuery = function (geneString) {
     let genes = "";
     let geneList = geneString.split(",");
-    geneList.forEach(x => genes += ("standardname=\'" + x + "\' OR "));
+    geneList.forEach(x => genes += ( `(fall2021.gene.display_gene_id =\'${x}\') OR `));
     return genes.substring(0, genes.length - 4);
 };
 
 let buildQuery = function (dataset, timepoints, genes) {
     return timepoints ?
-    `SELECT * FROM expressiondata WHERE dataset='${dataset}' AND
-    (${buildTimepointsQuery(timepoints)}) ORDER BY sortindex AND
-    (${buildGenesQuery(genes)}) ORDER BY sortindex;`
-    : `SELECT * FROM expressiondata WHERE dataset='${dataset}'
-    AND (${buildGenesQuery(genes)}) ORDER BY sortindex;`;
+    `SELECT *  FROM fall2021.expression, fall2021.gene WHERE fall2021.expression.dataset='${dataset}' AND
+    (${buildTimepointsQuery(timepoints)}) AND
+    ((${buildGenesQuery(genes)}) AND fall2021.gene.gene_id = fall2021.expression.gene_id) ORDER BY sort_index;`
+    : `SELECT * FROM fall2021.expression, fall2021.gene WHERE fall2021.expression.dataset='${dataset}'
+    AND ((${buildGenesQuery(genes)}) AND fall2021.gene.gene_id = fall2021.expression.gene_id) ORDER BY sort_index;`;
 };
 
 let listGeneData = function (gene, totalOutput) {
     let listOfData = [];
     totalOutput.forEach(function (x) {
-        if (x.standardname === gene) {
+        if (x.display_gene_id === gene) {
             listOfData.push(Number(x.expression));
         }
     });

package/server/controllers/exporters/xlsx.js

@@ -76,10 +76,22 @@ const buildMetaSheet = function (metaDataContainer) {
     return meta;
 };
 
+const EXPRESSION_SHEET_SUFFIXES = ["_expression", "_optimized_expression", "_sigmas"];
+
+const isExpressionSheet = (sheetName) => {
+    return EXPRESSION_SHEET_SUFFIXES.some(function (suffix) {
+        return sheetName.includes(suffix);
+    });
+};
+
 const buildExpressionSheets = function (expressions) {
     const builtExpressionSheets = [];
     Object.keys(expressions).forEach((expression) => {
-        const builtSheet = { name: expression, data: []};
+        let expressionName = expression;
+        if (!isExpressionSheet(expression)) {
+            expressionName = expression + "_expression";
+        }
+        const builtSheet = { name: expressionName, data: [] };
         Object.keys(expressions[expression]["data"]).forEach((key) => {
             const expressionData = expressions[expression]["data"][key];
             builtSheet["data"].push([key, ...expressionData]);
@@ -91,6 +103,7 @@ const buildExpressionSheets = function (expressions) {
 
 const buildXlsxSheet = function (workbook) {
     const resultSheet = [];
+    const exportNetworkType = workbook.exportNetworkType;
 
     Object.keys(workbook).forEach((key) => {
         switch (key) {
@@ -105,14 +118,16 @@ const buildXlsxSheet = function (workbook) {
             }
             break;
         case "networkOptimizedWeights":
-            if (Object.keys(workbook.networkOptimizedWeights).length > 0) {
-                resultSheet.push(
-                    {
-                        "name": "network_optimized_weights",
-                        "data": buildNetworkSheet(workbook.networkOptimizedWeights.genes,
-                            workbook.networkOptimizedWeights.links)
-                    }
-                );
+            if (exportNetworkType === "weighted") {
+                if (Object.keys(workbook.networkOptimizedWeights).length > 0) {
+                    resultSheet.push(
+                        {
+                            "name": "network_optimized_weights",
+                            "data": buildNetworkSheet(workbook.networkOptimizedWeights.genes,
+                                workbook.networkOptimizedWeights.links)
+                        }
+                    );
+                }
             }
             break;
         case "networkWeights":
@@ -150,6 +165,9 @@ const buildXlsxSheet = function (workbook) {
             resultSheet.push(...buildTestSheets(workbook[key]));
             break;
         case "expression":
+            // resultSheet.push(...buildExpressionSheets(workbook[key]));
+            break;
+        case "exportExpression":
             resultSheet.push(...buildExpressionSheets(workbook[key]));
             break;
         default:

package/test/export-tests.js

@@ -581,7 +581,7 @@ const inputWorkbook = {
     },
 
 
-    "expression": {
+    "exportExpression": {
         "wt_log2_expression": {
             "timePoints": [
                 0.4,
@@ -786,7 +786,7 @@ describe("Export to spreadsheet", function () {
             test.importFileSameAsExportFile(
                 "test-files/additional-sheet-test-files/optimization-diagnostics-default.xlsx");
             test.importFileSameAsExportFile(
-                "test-files/expression-data-test-sheets/expression_sheet_missing_data_ok.xlsx");
+                "test-files/expression-data-test-sheets/expression_sheet_missing_data_ok_export_exact.xlsx");
             test.importFileSameAsExportFile(
                 "test-files/additional-sheet-test-files/optimization-parameters-default.xlsx");
         }

package/test/test.js

@@ -716,16 +716,18 @@ var invalidMSEDataWarning = function (input, frequency) {
 var importExportReImportNoErrorsOrWarnings = function (input) {
     var sheet = xlsx.parse(input);
     var inputWorkbook = spreadsheetController.crossSheetInteractions(sheet);
+    inputWorkbook["exportExpression"] = inputWorkbook.expression;
     var exportedWorkbook = exportController.grnsightToXlsx(inputWorkbook);
     var sheet2 = xlsx.parse(exportedWorkbook);
     var reImportedWorkbook = spreadsheetController.crossSheetInteractions(sheet2);
-    // check if the re-imported workbook has no errors or warnings
     assert.equal(0, reImportedWorkbook.errors.length + reImportedWorkbook.warnings.length);
 };
 
 var importFileSameAsExportFile = function (input) {
     var sheet = xlsx.parse(input);
     var inputWorkbook = spreadsheetController.crossSheetInteractions(sheet);
+    inputWorkbook["exportExpression"] = inputWorkbook.expression;
+    inputWorkbook["exportNetworkType"] = inputWorkbook.sheetType;
     var exportedWorkbook = exportController.grnsightToXlsx(inputWorkbook);
     var sheet2 = xlsx.parse(exportedWorkbook);
     sheet.sort((a, b) => (a.name > b.name) ? 1 : -1);

package/web-client/app.js

@@ -16,7 +16,7 @@ var app = express();
 
 app.set("port", process.env.PORT || config.port || 3001);
 app.set("views", path.join(__dirname, "views"));
-app.set("view engine", "jade");
+app.set("view engine", "pug");
 
 app.use(morgan("dev"));
 app.use(bodyParser.urlencoded({extended: true}));

package/web-client/controllers/main.js

@@ -9,6 +9,6 @@ module.exports = function (app) {
     });
 
     app.get("/info", function (req, res) {
-        res.render("info", {title: "Test", serviceRoot: app.get("serviceRoot")});
+        res.render("info", {title: "Info", serviceRoot: app.get("serviceRoot")});
     });
 };

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

@@ -1,5 +1,7 @@
 export const HOST_SITE = "https://dondi.github.io";
 
+export const FILE_NAME = "#fileName";
+
 export const GREY_EDGES_DASHED_MENU = "#grey-edges-dashed-menu";
 export const GREY_EDGES_DASHED_SIDEBAR = "#dashedGrayLineButton";
 
@@ -13,7 +15,7 @@ export const SCHADE_INPUT_ID      = "#schadeInput";
 export const SCHADE_INPUT_PATH    = "demo/schadeInput";
 export const SCHADE_INPUT_NAME    = "Demo #3: Unweighted GRN (21 genes, 31 edges)";
 export const SCHADE_OUTPUT_ID     = "#schadeOutput";
-export const SCHADE_OUTPUT_PATH   = "demo/schadeOutput";
+export const SCHADE_OUTPUT_PATH = "demo/schadeOutput";
 export const SCHADE_OUTPUT_NAME   = "Demo #4: Weighted GRN (21 genes, 31 edges, Schade et al. 2004 data)";
 
 export const EXPORT_TO_EXCEL            = "#exportAsExcelWkbk";
@@ -25,6 +27,7 @@ export const EXPORT_TO_PNG              = "#exportAsPng";
 export const EXPORT_TO_SVG              = "#exportAsSvg";
 export const EXPORT_TO_PDF              = "#exportAsPdf";
 export const EXPORT_WEIGHTED_CLASS      = ".weighted.export";
+export const EXPRESSION_SOURCE          = "#expressionSource";
 
 export const DEMO_INFORMATION = [
     [ WEIGHTED_DEMO_ID,   WEIGHTED_DEMO_PATH,   WEIGHTED_DEMO_NAME   ],

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

@@ -104,6 +104,7 @@ import {
   VIEWPORT_SIZE_L_SIDEBAR,
   VIEWPORT_SIZE_FIT_SIDEBAR,
   VIEWPORT_INIT,
+//   EXPRESSION_SOURCE,
 } from "./constants";
 
 // In this transitory state, updateApp might get called before things are completely set up, so for now
@@ -349,7 +350,6 @@ const updateViewportSize = (currentValue) => {
         requestWindowDimensions();
     }
 };
-
 // Expression DB Access Functions
 const buildTimepointsString = function (selection) {
     let timepoints = "";
@@ -810,12 +810,8 @@ export const updateApp = grnState => {
                 responseData("", queryURLTop).then(function (response) {
                     grnState.workbook.expression[grnState.nodeColoring.topDataset] = response;
                     enableNodeColoringUI();
-
-                    if (grnState.nodeColoring.bottomDataSameAsTop ||
-                    !expressionDBDatasets.includes(grnState.nodeColoring.bottomDataset)) {
-                        stopLoadingIcon();
-                        updaters.renderNodeColoring();
-                    }
+                    stopLoadingIcon();
+                    updaters.renderNodeColoring();
                 }).catch(function (error) {
                     console.log(error.stack);
                     console.log(error.name);
@@ -865,10 +861,8 @@ export const updateApp = grnState => {
                     grnState.workbook.expression[grnState.nodeColoring.topDataset] = response;
                     enableNodeColoringUI();
 
-                    if (grnState.nodeColoring.bottomDataSameAsTop) {
-                        stopLoadingIcon();
-                        updaters.renderNodeColoring();
-                    }
+                    stopLoadingIcon();
+                    updaters.renderNodeColoring();
                 }).catch(function (error) {
                     console.log(error.stack);
                     console.log(error.name);
@@ -981,3 +975,6 @@ export const updateApp = grnState => {
     refreshApp();
 
 };
+
+
+export {buildURL, responseData, stopLoadingIcon};